Tag: BLAST

National Center for Biotechnology Information | Psychology Wiki

National Center for Biotechnology Information logo The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988. The NCBI houses genome sequencing data…

Continue Reading National Center for Biotechnology Information | Psychology Wiki

mcscanx

mcscanx 0 I have made files as per given in example blast and gff file xyz.blast contains: Eg01_t003090.1 Eg01_t003090.1 100.00 306 0 0 1 306 1 306 5e-173 594 Eg01_t003090.1 Eg01_t003100.1 98.38 309 2 1 1 306 1 309 1e-171 590 Eg01_t003090.1 Mba03_g02610.1 93.46 306 19 1 1 306 1…

Continue Reading mcscanx

The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms

1. The Plant List. The Plant List—A Working List of All Plant Species (Royal Botanic Gardens, Kew and Missouri Botanical Garden, 2019). www.theplantlist.org/. Retrieved 20 Aug 2019. 2. Christenhusz, M. J. M. & Byng, J. W. The number of known plants species in the world and its annual increase. Phytotaxa…

Continue Reading The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms

Chromosome-scale genome assembly of the high royal jelly-producing honeybees

1. Knecht, D. & Kaatz, H. H. Patterns of larval food production by hypopharyngeal glands in adult worker honey bees. Apidologie 21, 457–468, doi.org/10.1051/apido:19900507 (1990). Article  Google Scholar  2. Kamakura, M. Royalactin induces queen differentiation in honeybees. Nature 473, 478–483, doi.org/10.1038/nature10093 (2011). ADS  CAS  Article  PubMed  Google Scholar  3. Ramadan,…

Continue Reading Chromosome-scale genome assembly of the high royal jelly-producing honeybees

Compare two protein FASTA files and give a excel that show header with the same sequence

Compare two protein FASTA files and give a excel that show header with the same sequence 2 Dear All, I have two files file1.fasta file2.fasta. Both contain some identical sequences but different headers. I want to know the correspondence relationship between the headers of the two fasta files and may…

Continue Reading Compare two protein FASTA files and give a excel that show header with the same sequence

Benchmarking different approaches for Norovirus genome assembly in metagenome samples | BMC Genomics

Assembly Raw data obtained from eight human Norovirus samples passed FASTQC (v0.11.5, Babraham Bioinformatics) quality filters regarding the parameters per base sequence quality, per sequence average quality, N content and adapter sequences after the trimming steps described in the methods section. Mean read length was 100 bp as expected from library…

Continue Reading Benchmarking different approaches for Norovirus genome assembly in metagenome samples | BMC Genomics

Running Assembly Jobs on the Cluster with Checkpointing

Running Assembly Jobs on the Cluster with Checkpointing NERSC Tutorial 2/12/2013 Alicia Clum How We Use Genepool? • Assembly – Fungal, Microbial, Metagenome • • • Alignments Error correction Kmer matching/counting Tool benchmarking Data preprocessing – Linker trimming, changing quality formats, changing read formats, etc • Post assembly improvement •…

Continue Reading Running Assembly Jobs on the Cluster with Checkpointing

kseq compatible DNA fastA/Q encoding and compression library : bioinformatics

Hi all!! I would like to share with you this little project I have been working on for a while now. I would greatly appreciate if you find bugs or manage to break it with your own data. sqzlib is a little fastA/Q encoding library that uses zlib or zstd…

Continue Reading kseq compatible DNA fastA/Q encoding and compression library : bioinformatics

#1000359 – FTBFS: test failure: External MBEDTLS version mismatch

#1000359 – FTBFS: test failure: External MBEDTLS version mismatch – Debian Bug report logs Reported by: Stefano Rivera <stefanor@debian.org> Date: Mon, 22 Nov 2021 02:15:02 UTC Severity: serious Found in version python-biopython/1.79+dfsg-1 Fix blocked by 1000358: ncbi-blast+: Please remove the mbedtls version check Reply or subscribe to this bug. Toggle…

Continue Reading #1000359 – FTBFS: test failure: External MBEDTLS version mismatch

Please rebuild against MBEDTLS 2.16.11

Package: ncbi-blast+ Version: 2.11.0+ds-1 Severity: normal Affects: python-biopython Running blastn outputs: Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 runtime This causes python-biopython to FTBFS: ====================================================================== FAIL: test_blastn (test_NCBI_BLAST_tools.CheckCompleteArgList) Check all blastn arguments are supported. ———————————————————————- Traceback (most recent call last): File “/<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/Tests/test_NCBI_BLAST_tools.py”, line 420, in test_blastn self.check(“blastn”, Applications.NcbiblastnCommandline)…

Continue Reading Please rebuild against MBEDTLS 2.16.11

Fusion of the Paired Box 3 (PAX3) and Myocardin (MYOCD) Genes in Pediatric Rhabdomyosarcoma

Abstract Background/Aim: Fusions of the paired box 3 gene (PAX3 in 2q36) with different partners have been reported in rhabdomyosarcomas and biphenotypic sinonasal sarcomas. We herein report the myocardin (MYOCD on 17p12) gene as a novel PAX3-fusion partner in a pediatric tumor with adverse clinical outcome. Materials and Methods: A…

Continue Reading Fusion of the Paired Box 3 (PAX3) and Myocardin (MYOCD) Genes in Pediatric Rhabdomyosarcoma

Index of /~psgendb/local/biopython-1.64.old/Bio

Name Last modified Size Description Parent Directory   –   Affy/ 2014-05-29 05:25 –   Align/ 2014-06-11 10:27 –   AlignIO/ 2014-06-11 10:27 –   Alphabet/ 2014-06-11 10:27 –   Application/ 2014-05-29 05:25 –   Blast/ 2014-05-29 05:25 –   CAPS/ 2014-05-29 05:25 –   Cluster/ 2014-05-29 05:25 –  …

Continue Reading Index of /~psgendb/local/biopython-1.64.old/Bio

Genotyping of intraspecies polymorphisms of Sporothrix globosa using partial sequence of mitochondrial DNA – Mochizuki – – The Journal of Dermatology

1 INTRODUCTION Sporotrichosis is the most predominant and worldwide deep-seated dermatomycosis. The causative fungi, Sporothrix spp., which inhabits soil, causes lesions when inoculated into skin or subcutaneous tissue by tiny wounds. Sporothrix schenckii had long been regarded as the only species causing sporotrichosis until Marimon et al.1, 2 conducted molecular…

Continue Reading Genotyping of intraspecies polymorphisms of Sporothrix globosa using partial sequence of mitochondrial DNA – Mochizuki – – The Journal of Dermatology

blastn or tblastx for nucleotide blasts?

blastn or tblastx for nucleotide blasts? 1 When we have both a nucleotide query sequence and a nucleotide database is it best to use tblastx? I read that tblastx is superior because it helps account for wobble bases in codons, but in many publications I simply see people using blastn….

Continue Reading blastn or tblastx for nucleotide blasts?

blastn or tblastx for nucleotide blasts?

blastn or tblastx for nucleotide blasts? 1 When we have both a nucleotide query sequence and a nucleotide database is it best to use tblastx? I read that tblastx is superior because it helps account for wobble bases in codons, but in many publications I simply see people using blastn….

Continue Reading blastn or tblastx for nucleotide blasts?

Frontiers | Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs

Introduction Corn and soybean meal are the main components of high energy and high protein diets for pigs and are also the main raw materials of food products for human consumption, fermentation, and bioenergy industry (Sevillano et al., 2018). As the arable land of food crops was limited whereas the…

Continue Reading Frontiers | Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs

Frontiers | Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs

Introduction Corn and soybean meal are the main components of high energy and high protein diets for pigs and are also the main raw materials of food products for human consumption, fermentation, and bioenergy industry (Sevillano et al., 2018). As the arable land of food crops was limited whereas the…

Continue Reading Frontiers | Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs

(PDF) Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system | Charles Opperman

(PDF) Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system | Charles Opperman – Academia.edu Academia.edu uses cookies to personalize content, tailor ads and improve the user experience. By using our site, you agree to our collection of information through the use of cookies. To learn more, view our Privacy…

Continue Reading (PDF) Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system | Charles Opperman

Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae

1. Strassert, J. F. H., Irisarri, I., Williams, T. A. & Burki, F. A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids. Nat. Commun. 12, 1879 (2021). ADS  CAS  PubMed  PubMed Central  Google Scholar  2. Burki, F., Roger, A. J., Brown, M. W. &…

Continue Reading Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae

Age- and gender-independent association of XRCC1 Arg399Gln

Introduction Chronic myeloid leukemia (CML) is a member of myeloproliferative neoplasms characterized by the acquired reciprocal chromosomal translocation, t(9;22) (q34; q11) which occurs as a result of translocation of ABL1 (Abelson murine leukemia) gene from chromosome 9 and its fusion with the BCR (breakpoint cluster region) gene on chromosome 22.1…

Continue Reading Age- and gender-independent association of XRCC1 Arg399Gln

protein sequence database slideshare

The N-terminal amino acid of the protein can be cleaved off. As we can see from the image below, starting from the 1990ties, PDB content growth … A high quality sequence alignment gives the idea about Additionally most PMF algorithms assume that the peptides come from a single protein. Retrieve/ID…

Continue Reading protein sequence database slideshare

How to extract certain CDS from a GenBank file in linux terminal

How to extract certain CDS from a GenBank file in linux terminal 1 Hi, I have a large GenBank file that contains multiple records. I got this file after performing BLAST against my query sequence. This .gb file contains all the results (full record in GenBank format for each accession)…

Continue Reading How to extract certain CDS from a GenBank file in linux terminal

Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity

1. Hoegh-Guldberg, O. & Bruno, J. F. The impact of climate change on the world’s marine ecosystems. Science 328, 1523–1528 (2010). CAS  PubMed  Google Scholar  2. Chou, C. et al. Increase in the range between wet and dry season precipitation. Nat. Geosci. 6, 263–267 (2013). CAS  Google Scholar  3. Li,…

Continue Reading Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity

16S rRNA merge forward and reverse primers

16S rRNA merge forward and reverse primers 2 Hi all, I have received 16S rRNA sequencing data for ~ 100 samples. I want to use these sequences to identify the samples to genus level using the NCBI BLAST 16s bacteria and archaea database. For each sample I have a forward…

Continue Reading 16S rRNA merge forward and reverse primers

16S rRNA merge forward and reverse primers

16S rRNA merge forward and reverse primers 2 Hi all, I have received 16S rRNA sequencing data for ~ 100 samples. I want to use these sequences to identify the samples to genus level using the NCBI BLAST 16s bacteria and archaea database. For each sample I have a forward…

Continue Reading 16S rRNA merge forward and reverse primers

I have a problem with blastx against database nr.

I have a problem with blastx against database nr. 1 -Hello -I built the database for the nr with the following command $ makeblastdb -dbtype prot -in nr -which went well and generated .pal .psq files. phr -then I ran the blastx with the following command $blastx -db nr -query…

Continue Reading I have a problem with blastx against database nr.

Set database size in MMseqs2 (like -dbsize in blast)

Set database size in MMseqs2 (like -dbsize in blast) 0 Hello all, I would like to search a sequence database using MMseqs2. Because the database might change in size during my analyses, I would like to be able to specify a fixed database size to avoid creating inconsistencies in reported…

Continue Reading Set database size in MMseqs2 (like -dbsize in blast)

BLAST help : bioinformatics

Hello I’m an undergrad Biochem student and we’re currently learning about how to use BLAST and interpreting the result and I’m quite confused about how to interpret the result. So I got a set of DNA sequence that belongs to Drosophila and the task is to identify the gene using…

Continue Reading BLAST help : bioinformatics

Different gene rearrangements of the genus Dardanus (Anomura: Diogenidae) and insights into the phylogeny of Paguroidea

1. Boore, J. L. Animal mitochondrial genomes. Nucl. Acids Res. 27, 1767–1780 (1999). CAS  PubMed  PubMed Central  Article  Google Scholar  2. Gyllensten, U., Wharton, D., Josefsson, A. & Wilson, A. C. Paternal inheritance of mitochondrial DNA in mice. Nature 352, 255–257 (1991). ADS  CAS  PubMed  Article  PubMed Central  Google Scholar …

Continue Reading Different gene rearrangements of the genus Dardanus (Anomura: Diogenidae) and insights into the phylogeny of Paguroidea

Presence absence matrix from blast results

Presence absence matrix from blast results 0 I have a many blast output files of genome names, which looks like this. In the first column of the file, it contains all the identified query UIDs, I want to make a presence-absence matrix in csv format in which a column would…

Continue Reading Presence absence matrix from blast results

How to identify corresponding chromosomes and coordinates of a species for query genes from a another species

How to identify corresponding chromosomes and coordinates of a species for query genes from a another species 0 I have a list of genes from species A and reference genome and gff3 of species B. I want to know homologous genes of species A genes in species B. I am…

Continue Reading How to identify corresponding chromosomes and coordinates of a species for query genes from a another species

blastp Error: NCBI C++ Exception: ncbi::CObject::ThrowNullPointerException()

blastp Error: NCBI C++ Exception: ncbi::CObject::ThrowNullPointerException() – Attempt to access NULL pointer 0 Hi, I am trying to blast a fasta file of protein sequences against the non-redundant database on a HPC. I run the following command: cat prot/split_fasta/master.dataframe.tide-tandem.protein.part_001.fa | parallel –GNU –block 100k –recstart ‘>’ –pipe ‘/home/users/nus/e0470749/ncbi-blast-2.8.1+/bin/blastp -query –…

Continue Reading blastp Error: NCBI C++ Exception: ncbi::CObject::ThrowNullPointerException()

Help for extraction of fasta sequences

Hello everyone, I hope you are well. I am writing this post because I have a question or rather I have a problem with my workflow. Perform a workflow for RNA-seq processing as follows: quality control – Hisat2 – Stringtie – Deseq2 A simple, normal workflow that threw me important…

Continue Reading Help for extraction of fasta sequences

How does orthomclBlastParser output looks like

How does orthomclBlastParser output looks like 1 Hello everyone, I am running Orthomcl in the set of proteomes I am working on and now I am in orthomclBlastParser step. The output that I got from blastp is in m-8 format as specified by the maual. head blastp.out T415|100119 HDV247|16147 100.000…

Continue Reading How does orthomclBlastParser output looks like

Detection of heteroplasmy and nuclear mitochondrial pseudogenes in the Japanese spiny lobster Panulirus japonicus

Direct nucleotide sequencing Readable electropherograms were obtained from both direction in COI fragments of all three individuals of the Japanese spiny lobster. COI sequences determined by direct nucleotide sequencing ranged from 807 to 864 bp and have been deposited in International Nucleotide Sequence Database Collection (INSDC) under accession numbers of LC571524‒LC571526….

Continue Reading Detection of heteroplasmy and nuclear mitochondrial pseudogenes in the Japanese spiny lobster Panulirus japonicus

Unexpected blastx results

Unexpected blastx results 1 Hi. I ran blastx with 10 results for each sequence. I noticed 2 issues with the results: 1) For most input sequences, each sequence got results for the same gene / protein, which is unlike in blastn in which every input sequence got multiple results. For…

Continue Reading Unexpected blastx results

Bioinformatics_lab_HANDOUT_and_worksheet 2020.doc – BIO214 Lab9 Bioinformatics Lab Assignment(20 pts Name BIOINFORMATICS Biological information is

BIO214 Name:___________________________ Lab9: Bioinformatics Lab Assignment (20 pts) BIOINFORMATICS Biological information is encoded in the nucleotide sequence of DNA. Bioinformatics is the field that identifies biological information in DNA using computer-based tools. Some bioinformatics algorithms aid the identification of genes, promoters, and other functional elements of DNA. Other algorithms help…

Continue Reading Bioinformatics_lab_HANDOUT_and_worksheet 2020.doc – BIO214 Lab9 Bioinformatics Lab Assignment(20 pts Name BIOINFORMATICS Biological information is

Samtools Samtools Statistics & Issues

  Issue TitleStateCommentsCreated DateUpdated DateClosed Datesamtools 1.10 csi vs 1.13 generation/reading closed 22021-11-012021-10-272021-11-03mpileup: –output-BP-5 switches output column 7 and 8 open 22021-11-012021-10-27-ampliconclip bug when hardclipping odd-length sequences from the left closed 12021-10-232021-10-272021-11-03Feature Request: Flag in ampliconclip to clip out everything except target sequence open 22021-10-222021-10-27-samtools markdup slow in docker open…

Continue Reading Samtools Samtools Statistics & Issues

Molecular Characterisation of Class 1, 2 and 3 Integrons

Introduction Gram-negative rods of the genus Serratia are environmental bacteria which play an increasing role as etiological agents of healthcare-associated infections (HAI). These bacteria were previously classified in the family Enterobacteriaceae, but due to 2016 taxonomy change, the genus Serratia at present belongs to the newly formed family Yersiniaceae in…

Continue Reading Molecular Characterisation of Class 1, 2 and 3 Integrons

makeblastdb Error: ncbi::objects::CSeq_id::x_Init() – Unsupported ID type 1196094

Blast is rather picky about identifiers. As soon as you have identifiers containing pipes |, it assumes your are trying to give it NCBI-style identifiers. But the behavior of makeblastdb may have changed slightly, so I tested a few options. Also, makeblastdb will only report the first error it encounters….

Continue Reading makeblastdb Error: ncbi::objects::CSeq_id::x_Init() – Unsupported ID type 1196094

Jgi Portal – LoginWave

If you are looking for jgi portal, simply check out our links below : genome.jgi.doe.gov/ Genomes Online Database Genome Portal The JGI Genome Portal provides unified access to all JGI genomic databases and analytical tools. A user can search, download and explore multiple data sets … img.jgi.doe.gov/ JGI Genome Portal –…

Continue Reading Jgi Portal – LoginWave

main-armv6-default][biology/p5-BioPerl] Failed for p5-BioPerl-1.007007_1 in stage

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: sunp…@freebsd.org Log URL: beefy8.nyi.freebsd.org/data/main-armv6-default/pebf5105f9a4d_s23024f004a/logs/p5-BioPerl-1.007007_1.log Build URL: beefy8.nyi.freebsd.org/build.html?mastername=main-armv6-default&build=pebf5105f9a4d_s23024f004a Log: =>> Building biology/p5-BioPerl build started at Fri Oct 29…

Continue Reading main-armv6-default][biology/p5-BioPerl] Failed for p5-BioPerl-1.007007_1 in stage

How to use python blast to search for protein homologs and retrieve 10 of it?

How to use python blast to search for protein homologs and retrieve 10 of it? 1 I am new for bioinformatics, and I want to use python to blast for protein homolog. After I save the result in xml file, I don’t know how to retrieve the nucleotide sequence from…

Continue Reading How to use python blast to search for protein homologs and retrieve 10 of it?

How to filter blast results by BioSample attributes via CLI? (Searching for bacterial genes from specific habitats )

How to filter blast results by BioSample attributes via CLI? (Searching for bacterial genes from specific habitats ) 0 I have the nucleotide sequence of a protein of interest, and I’d like to search for orthologs present in bacteria from specific habitats (e.g. thermal springs) using blast command line tools….

Continue Reading How to filter blast results by BioSample attributes via CLI? (Searching for bacterial genes from specific habitats )

AKIRIN2 controls the nuclear import of proteasomes in vertebrates

1. Johnston, L. A., Prober, D. A., Edgar, B. A., Eisenman, R. N. & Gallant, P. Drosophila myc regulates cellular growth during development. Cell 98, 779–790 (1999). CAS  PubMed  Article  Google Scholar  2. Sabo, A. et al. Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis. Nature 511,…

Continue Reading AKIRIN2 controls the nuclear import of proteasomes in vertebrates

There is a problem with the BLASTN xml output

Based on biojava, I personally made and am using something that works with blastN. I was using the NR and NT DB of v4 locally. However, there was one problem after updating this v5. I tried to read and xml the pasta file with version 2.11.0 of BLAST+. (This is…

Continue Reading There is a problem with the BLASTN xml output

Lead Data Scientist – Bioinformatics job with Spark Therapeutics

Primary Duties The Bioinformatics Group within the Data Science Organization at Spark Therapeutics is seeking an engaged and passionate Lead Data Scientist with a focus on bioinformatics and computational biology to participate in and support projects involving omics and other high-dimensional data across the Technology & Research Organizations. He/she will…

Continue Reading Lead Data Scientist – Bioinformatics job with Spark Therapeutics

Gene ontology from annotation

Gene ontology from annotation 2 Hello, I am needing some help identifyng the GO of a gene. I have a cordinate for the gene, I just need to find its GO using the loci info. Is that doable? function non-model animal GO gene • 67 views Once upon a time,…

Continue Reading Gene ontology from annotation

blastn alighment gives error while excluding sequence from local database by seqidlist

Hello Biostar community, I have several .fa sequences I and I want to check if they have some homology, e.g. if they align within each other. To do so, I concatenate all sequences in a single .fa file, create a database on it, and run blast of the interested .fasta…

Continue Reading blastn alighment gives error while excluding sequence from local database by seqidlist

Is ther a tool to compare protein identities between two nearly identical proteomes?

Is ther a tool to compare protein identities between two nearly identical proteomes? 1 Hi all, I’m looking for a tool to compare two fungal proteomes. The proteome set consists of around 11,000 different proteins each that were predicted in-silico from two sequencing experiments. One is from a parent fungal…

Continue Reading Is ther a tool to compare protein identities between two nearly identical proteomes?

Junior Bioinformatician at the Lymphoma Genomic Laboratory

Junior Bioinformatician at the Lymphoma Genomic Laboratory Open position Junior Bioinformatician at the Lymphoma Genomic Laboratory Institute of Oncology Research (IOR) Bellinzona, Switzerland www.ior.usi.ch www.ior.usi.ch The Institute of Oncology Research (IOR) in Bellinzona, Switzerland, is a rapidly evolving,leading center for basic and translational research in oncology in Europe.IOR is affiliated…

Continue Reading Junior Bioinformatician at the Lymphoma Genomic Laboratory

BLAST+ v2.10.1 file accessibility

Hello, I am trying to use BLAST+ v2.10.1 as part of a pipeline I’ve built. When I call it via subprocess I get this error: ApplicationError: Non-zero return code 1 from ‘C:\Users\my_username\.spyder-py3\my_pipeline\Backend\Executables\NCBI\blast-2.10.1+\bin\blastp.exe -out C:\Users\my_username\.spyder-py3\my_pipeline\Backend\Intermediate_files\reverse_blast\BLASTP_results\AS6_Streptomyces_griseochromogenes_ATCC_14511\json_AS6_Streptomyces_griseochromogenes_ATCC_14511__genome_number_1__genome_id_CP016279.1__for__results_reverse.xml -outfmt 5 -parse_deflines -query C:\Users\my_username\.spyder-py3\my_pipeline\Backend\Intermediate_files\reverse_blast\BLASTP_queries\AS6_Streptomyces_griseochromogenes_ATCC_14511\json_AS6_Streptomyces_griseochromogenes_ATCC_14511__genome_number_1__genome_id_CP016279.1__for_reverse_query.txt -db C:\Users\my_username\.spyder-py3\my_pipeline\Backend\Intermediate_files\reverse_blast\BLASTP_db\AS6_Streptomyces_griseochromogenes_ATCC_14511\json_AS6_Streptomyces_griseochromogenes_ATCC_14511__genome_number_1__genome_id_CP016279.1__for_reverse_db -evalue 1e-06 -num_threads 4’, message ‘Command line argument error:…

Continue Reading BLAST+ v2.10.1 file accessibility

History of Changes for Study: NCT01119586

Study Identification Unique Protocol ID: AALL10B2 Brief Title: Biomarkers in DNA Samples From Patients With High-Risk Acute Lymphoblastic Leukemia Official Title: Identifying Rare Genetic Variants Involved in High Risk Acute Lymphoblastic Leukemia (ALL) Via Pooled DNA Sequencing Secondary IDs: COG-AALL10B2 [Children’s Oncology Group]CDR0000672526 [Clinicaltrials.gov]NCI-2011-02232 [Registry Identifier: CTRP (Clinical Trial Reporting…

Continue Reading History of Changes for Study: NCT01119586

How to use a downloaded BLAST database

How to use a downloaded BLAST database 0 Hi, I am trying to BLAST some sequences against all the virus and prokaryote genomes available in NCBI. I found out that there are existing BLAST databases for both of them that can be downloaded from BLAST (ftp.ncbi.nlm.nih.gov/blast/db/) I downloaded the virus…

Continue Reading How to use a downloaded BLAST database

PER1 as a Tumor Suppressor Attenuates Breast Cancer

Introduction Breast cancer is one of the most common malignancies in women, with a high mortality rate around the world.1,2 Although multidisciplinary therapeutic strategies, including surgical resection, chemoradiotherapy, endocrine and anti-HER2 therapy, have made substantial progress over the past decade, there are still a considerable proportion of breast cancer patients…

Continue Reading PER1 as a Tumor Suppressor Attenuates Breast Cancer

LncRNA MIAT services as a noninvasive biomarker

Introduction BC is the most common cancer among women that is responsible for the most of the cancer-related death in worldwide.1 The occurrence of BC accounts for 7–8% of the entire number of malignant tumors.2 Accumulating evidence have shown that immunoreaction plays an important role in oncogenesis and progression.3,4 However,…

Continue Reading LncRNA MIAT services as a noninvasive biomarker

Would you please give me some advices about how to change header?

Would you please give me some advices about how to change header? 2 Hi, all. I would like to edit headers from fasta. I have fasta with random header as following(headers are separated by space); >3R5.1a wormpep=CE24758 gene=WBGene00007065 locus=pot-3 status=Confirmed uniprot=G5EFG7 insdc=CAA21777.2 product=”POT1PC domain-containing protein” >2RSSE.1a wormpep=CE32785 gene=WBGene00007064 locus=rga-9 status=Confirmed…

Continue Reading Would you please give me some advices about how to change header?

qPCR primer design for multiple transcript variants

qPCR primer design for multiple transcript variants 0 Hello, I am a little new to NCBI tools and can’t quite wrap my head around primer design on the website. I am trying to design primers to run single-step qPCR for one gene’s expression. There are 3 transcript variants, all of…

Continue Reading qPCR primer design for multiple transcript variants

Cant make blastn work using biopython and NCBIWWW qblast, any thoughts?

Hello all, I’m a beginner level python user experiencing a problem using biopython. I’m taking an online bioinformatics course and the example that we’re working through right now is to take a fasta file (called myseq.fa in the following example), open it then read. Then using the NCBIWWW module we…

Continue Reading Cant make blastn work using biopython and NCBIWWW qblast, any thoughts?

the way to find pseudogenes in my scaffolds of genome

the way to find pseudogenes in my scaffolds of genome 3 Hello Recently, I assembled genome of a beetle living underground. My interest is searching pseudogenes (premature stop codon or frameshifts). I conducted tblastn using a few genes of model organisms (Tribolium) as query. But no premature stop codons were…

Continue Reading the way to find pseudogenes in my scaffolds of genome

KOBAS on Galaxy local

KOBAS on Galaxy local 0 Hello, I’m trying to setting up Galaxy on my PC. I need to use the tool “KOBAS annotate” & “KOBAS identify”. I would need help in setting up the field “BLAST protein database” since I don’t understand how to configure it. I tried to download…

Continue Reading KOBAS on Galaxy local

Blastx only uses one thread when word size is above 3

Blastx only uses one thread when word size is above 3 0 Hi all, I’m using blast version 2.12.0 and running the following command blastx -db my_db -query ecoli.fna -num_threads 8 -word_size 3 The query runs pretty fast and if I check the CPU usage is always around 600-700%. However,…

Continue Reading Blastx only uses one thread when word size is above 3

How do I get description in BLAST?

How do I get description in BLAST? 0 Hi, all. I’m trying to get a description to the gene list using BLAST. I created the original database with the following command and did BLAST, but my output shows a lot of N/A. $ makeblastdb -in caenorhabditis_elegans.PRJNA13758.WBPS16.protein.fa -out elegansdb -dbtype prot…

Continue Reading How do I get description in BLAST?

What is eggnog better than previous annotation in terms of?

What is eggnog better than previous annotation in terms of? 0 Hi, all. I used eggnog to get annotations in de novo RNAseq analysis But I haven’t understand the merit. What is eggnog better than previous annotation(ex. BLAST etc.) in terms of? Although I had read ths instruction in eggnog,…

Continue Reading What is eggnog better than previous annotation in terms of?

What is the best gun mod for GMOD?

[Top 10] Garrys Mod Best Weapon Addons Every Player Needs Customizable weaponry 2.0 – Khris’s Weapons – Full Package. No. Air To Surface Missile. RAMIREZ! … [TFA] Dead Space 2 Weapons. They’re coming out of the walls! … Tactical Baby Weapons. … WW2 Weapons Part 2. … Some throwable weapons….

Continue Reading What is the best gun mod for GMOD?

Restrict blastp search to set of specific species

Restrict blastp search to set of specific species 1 I want to perform a blastp search on a set of around 200 representative species with a list of known taxids. Is it possible using the web browser version of blast to efficiently limit my search without manually entering each of…

Continue Reading Restrict blastp search to set of specific species

Learn Biopython: Preliminary Step Toward Bioinformatics

MP4 | Video: h264, 1280×720 | Audio: AAC, 44.1 KHz, 2 Ch Genre: eLearning | Language: English + .srt | Duration: 32 lectures (2h 28m) | Size: 815 MB Performing the Daily Tasks of Bioinformatics What you’ll learn: The basics of Python and Biopython Requirements There are no requirements except…

Continue Reading Learn Biopython: Preliminary Step Toward Bioinformatics

Practical value of bits and SW-score in KEGG

Practical value of bits and SW-score in KEGG 1 Hello, Can someone explain to me the practical value of bits and SW-score in KEGG? What does it actually mean for my sequence? The image below shows paralogs table as shown in the base what is the practical value of these…

Continue Reading Practical value of bits and SW-score in KEGG

Plot Blastn.table file on R

Hi I’m trying to find a way to plot the results of my blastn script (.table output file). The output file is quite big since I had to characterize more than 200 gRNA target sites. The file contains also a lot of duplicated hits on the subject column and i…

Continue Reading Plot Blastn.table file on R

BLAST Results, location on genome

BLAST Results, location on genome 0 Hi, I’m visualizing a genome, and i have to be able to get from a blast search result to the location of the hit. So im running a BLAST instance locally, and I already generated a BLAST db. Searching against this db works, but…

Continue Reading BLAST Results, location on genome

NGSeq/DHPGIndex: This tool is for compressing and indexing pan-genomes and genome sequence collections for scalable sequence and read alignment purposes.

General This tool is for compressing and indexing pan-genomes and genome sequence collections for scalable sequence and read alignment purposes. The pipeline can be deployed in cloud computing environment or in dedicated computing cluster. The tool extends the CHIC aligner gitlab.com/dvalenzu/CHIC with distributed and scalable features. DHPGIndex have been tested…

Continue Reading NGSeq/DHPGIndex: This tool is for compressing and indexing pan-genomes and genome sequence collections for scalable sequence and read alignment purposes.

Protein Sequences MSA vs. BLASTp

Protein Sequences MSA vs. BLASTp 0 Hello everyone here! I am recently working on ligand discovery. What I’m doing now is to find out if the ligand which targets the pathogen’s specific enzyme will also have effect on human’s. I do BLAST to pathogen’s protein to look for similar proteins…

Continue Reading Protein Sequences MSA vs. BLASTp

Tumor Biology Lab Research Associate Job at UC San Diego Health

– Advertisement – Tumour Biology Lab Research Associate Job at UC San Diego Health Filing Deadline: Mon 10/18/2021 For the safety and well-being of the entire university community, the University of California requires, with few exceptions, that all students, faculty and staff be vaccinated against the COVID-19 virus before they…

Continue Reading Tumor Biology Lab Research Associate Job at UC San Diego Health

The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests

Sequencing of Shorea leprosula genome Sample collection Leaf samples of S. leprosula were obtained from a reproductively mature (diameter at breast height, 50 cm) diploid tree B1_19 (DNA ID 214) grown in the Dipterocarp Arboretum, Forest Research Institute Malaysia (FRIM). DNA extraction Genomic DNA was extracted from leaf samples using the…

Continue Reading The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests

Blast applications analysis at MainKeys

add to compare Best Penny Stock, Best SEO Company New York, Marketing Company New York blastapplications.com Blastapplications is one of the largest Best Penny Stock New York, Best SEO Company New York, Marketing Company New York best seo company new York. And much more. 0  add to compare InvestorsHub –…

Continue Reading Blast applications analysis at MainKeys

filtering results by a minimum % of identity and % coverage

BLASTp command line : filtering results by a minimum % of identity and % coverage 0 Hi all, I use regularly BLASTp analysis and I would like to improve my command line so that only resulting hits with 60% of similarity and 60 % of coverage appear in the output…

Continue Reading filtering results by a minimum % of identity and % coverage

Quantitative PCR assay for detection of Helicobacter pylori

Introduction Helicobacter pylori is a common pathogen that infects nearly 50% of the global population.1 Infection with this pathogen causes chronic gastritis, which can cause chronic gastroduodenal diseases such as gastritis, gastric ulcer, duodenal ulcer, gastric cancer, and gastric mucosa-associated lymphoid tissue (MALT) B-cell lymphoma.2 Although H. pylori is the…

Continue Reading Quantitative PCR assay for detection of Helicobacter pylori

Gmod Vj Cars

Jan 13, 2008 · As “Gmod N” A map of groups ˚ (G 1;) !(G 2;1312 · Garry’s Mod Store Page Garry’s Mod > Workshop > Hoodwink abuser’s Workshop This item has been removed from the community because it violates Steam Community & Content Guidelines It is only visible to you…

Continue Reading Gmod Vj Cars

How To Extract A Sequence From A Big (6Gb) Multifasta File ?

How To Extract A Sequence From A Big (6Gb) Multifasta File ? 11 I want to extract some sequences using ID from a multifasta file. Using perl is not possible because it gave an error when indexing the database. Maybe because of it’s size? Is there any way to this…

Continue Reading How To Extract A Sequence From A Big (6Gb) Multifasta File ?

Inferring homology from BLAST scores/statistics : bioinformatics

Hello, I have some proteins with blast homologs, and I am trying to get a quantitative measure of the representativeness of each match. As I understand, everyone normally compares blast alignments using bit scores, as these are database-size independent. However (please correct me if I’m wrong) bit-scores only describe the…

Continue Reading Inferring homology from BLAST scores/statistics : bioinformatics

Inferring homology from BLAST scores/statistics

Inferring homology from BLAST scores/statistics 0 Hello, I have some proteins with blast homologs, and I am trying to get a quantitative measure of the representativeness of each match. As I understand, everyone normally compares blast alignments using bit scores, as these are database-size independent. However (please correct me if…

Continue Reading Inferring homology from BLAST scores/statistics

blast protein alignment

28 set blast protein alignment Posted at 20:44h in Sem categoria by BLAST applied the standard genetic code for Query, translating GTG into valine (V). The BLAST is a set of algorithms that attempt to find a short fragment of a query sequence that aligns perfectly with a fragment of…

Continue Reading blast protein alignment

Blast Portal – LoginWave

If you are looking for blast portal, simply check out our links below : blast.ncbi.nlm.nih.gov/The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to … blastconnect.com/ Blast Connect is an information analysis, reporting, player management, and coaching application for…

Continue Reading Blast Portal – LoginWave

How to make BLASTN be aware of short read?

I’m using blastn (anaconda.org/bioconda/blast) to find similar sequences of a target sequence against a FASTA file. But my read is quite short (68 bases). I realised that blastn won’t report any hit. But there is actually a very good one in the FASTA file after checking manually. Here is the…

Continue Reading How to make BLASTN be aware of short read?

Are BLAST search parameters recorded in the XML file?

Are BLAST search parameters recorded in the XML file? 1 Hi, I have XML files from BLASTn searches but I’m not sure what, if any, parameters were selected. Would this be recorded in the file? I’m specifically interested in if a different “Max target sequences” was selected. How might I…

Continue Reading Are BLAST search parameters recorded in the XML file?

Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach

Genome assembly In this study, we de novo assembled the plum, Prunus mira, and Prunus davidiana genomes for the first time and improved the peach and apricot genomes by integrating single-molecule real-time (SMRT) long-read sequencing (PacBio), short high-quality Illumina paired-end sequencing, and Hi-C technology. First, we used SMRT reads (99−130 Gb,…

Continue Reading Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach

Mutational profile of the dystrophin gene

Introduction Duchenne Muscular Dystrophy (DMD-OMIM #310200) and Becker Muscular Dystrophy (BMD-OMIM #300376), are the most common hereditary muscular dystrophies around the world.1 DMD and BMD occur with a frequency of 1/3.300 and 1/6.000 newborn males, respectively.2 These dystrophinopathies are caused by alterations in the DMD gene and have an X-linked…

Continue Reading Mutational profile of the dystrophin gene

Unraveling the hidden role of a uORF-encoded peptide as a kinase inhibitor of PKCs

Short open reading frames (ORF) upstream of the canonical ORF (uORFs) are found in about 40% of human protein-coding transcripts (1⇓–3). uORF-containing genes were shown to participate in heavily regulated processes, including differentiation, cell cycle control, and stress responses (4⇓–6). Ribosome profiling data revealed that many uORFs are translated (3,…

Continue Reading Unraveling the hidden role of a uORF-encoded peptide as a kinase inhibitor of PKCs

Is there really a difference in blastn -task blastn and -task megablast when dealing with unmapped reads?

Forum:Is there really a difference in blastn -task blastn and -task megablast when dealing with unmapped reads? 0 Hi all, I’ve been running a variety of blastn options with my metagenomic dataset with the goal of trying to find the best hits for my contigs (produced from metaspades). I’ve recently…

Continue Reading Is there really a difference in blastn -task blastn and -task megablast when dealing with unmapped reads?

Pathway Hole Filler

Pathway Hole Filler 0 Hello, I am using Pathway Tools v 25.0 and I am trying to run the Pathway Hole filler on my database. However, each time I tried to run it, the hole filler failed. I got the error message: PathoLogic is unable to prepare BLAST protein data….

Continue Reading Pathway Hole Filler

install biopython jupyter

like BLAST, ClustalW, FASTA, GenBank, PubMed ExPASy, SwissProt, and many more. conda install-c conda-forge ipyleaflet With pip: pip install ipyleaflet If you are using the classic Jupyter Notebook >> import Bio >>> Bio.__version__. For Windows we provide click-and-run installers. The easiest way to install statsmodels is to install it as…

Continue Reading install biopython jupyter

biopython write fasta

Step 1 − Create a file named blast_example.fasta in the Biopython directory and give the below sequence information as input. 3. “””Bio.SeqIO support for the “fasta” (aka FastA or Pearson) file format. Then we save this line of text to the output file: Now we have finished all the genes,…

Continue Reading biopython write fasta

genbank submission tutorial

These are just a few of the questions answered in this comprehensive overview of Bayesian approaches to phylogenetics. Finally, make sure the Include Primers box is unchecked, as we are not submitting primers with this sequence. Influenza virus sequences. September, 2008. Please download the current version. Some mitochondrial genomes contain CDS’s that…

Continue Reading genbank submission tutorial

How to verify putative miRNA

How to verify putative miRNA 1 My PI gave me a list of some DNA sequences, each one around 25 nucleotides, that are suspected to code for Vitis Vitinesfera miRNA. To know if they are complementary to some mRNA for a known protein sequence, we do the following process: BLAST…

Continue Reading How to verify putative miRNA

How do you get the result of BLAST like this paper?

Since you’re blasting with ncbi-NR you’re almost there. By changing the blastx output options to outfmt 6 you’re receiving tabular output in avenae.out, you can customise the output columns to also receive the species names. For example, you could run: blastx -query /home/nkarim/avenae/trinity_even_out_dir/Trinity.300.longest.fasta -db /home/nkarim/blast/db/nr -outfmt “6 qseqid sseqid sscinames…

Continue Reading How do you get the result of BLAST like this paper?

bioinformatician jobs

1 The first category includes developers who implement algorithms and develop tools for bioinformatics. Simply put, it has just the right breadth and depth, and it reads well. In fact, readability is one of its virtues—making the book enticing and useful, all at once…” Human Vaccines, 2010 “… This book…

Continue Reading bioinformatician jobs

bioinformatics analyst entry level

The average bioinformatics analyst salary is $71,298 per year, or $34.28 per hour, in the United States. $12.75 – $24.25. Bioinformatics Analyst. Jobs Limited to Sustainable Energy. Proficiency in programming in C, C++, C#, or Java. Create more job alerts for related jobs with one click: Junior to Mid-level Patent…

Continue Reading bioinformatics analyst entry level

genbank database slideshare

Found inside – Page iiThis book describes the historical importance of potato (Solanum tuberosum L.),potato genetic resources and stocks (including S. tuberosum group Phureja DM1-3 516 R44, a unique doubled monoploid homozygous line) used for potato genome … If you continue browsing the site, you agree to the use of…

Continue Reading genbank database slideshare

genbank submission bankit

Submission of sequence data to NCBI archives . Learn more. This post will show you how to… Careers, General: your contact details, authors, publication, data release date, Original or third-party assembly/annotation, Set designation (if applicable) for multiple sequences of the same locus, Nucleotide sequences in FASTA or alignment format, Source…

Continue Reading genbank submission bankit

biopython extract sequence from fasta

My two questions are: What is the simplest way to do this? This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. using python-bloom-filter, just replace the set with seen = BloomFilter(max_elements=10000, error_rate=0.001). This book is suitable for use as a classroom textbook,…

Continue Reading biopython extract sequence from fasta