Tag: EMBOSS

  Q&A Report from the workshop: QuestonWha is he bes msa ool?clusal 2 and clusal omega are he sameHow would we ener multple sequences? because here is only one inpu boxCould he legend explaining symbiols (*, -,…) be shown in he resul window?Wha is he max number of sequences one…

Prediction with AlphaFold2 and AlphaFold-Multimer For each PDB the release date in the Protein Data Bank34 was recorded. AlphaFold 2 (2.2.2) was run setting the –max_template_date flag to be the day before the release date of the PDB and the –model_preset to be either monomer for AF or multimer for…

Zachos, J., Pagani, H., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001). Article  ADS  CAS  PubMed  Google Scholar  Favre, A. et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan…

Name Last modified Size Description Parent Directory   –   acnum.hit 2011-08-16 10:59 620   acnum.trg 2011-08-16 10:59 1.5K   des.hit 2011-08-16 10:59 1.6K   des.trg 2011-08-16 10:59 4.9K   division.lkp 2011-08-16 10:59 520   entrynam.idx 2011-08-16 10:59 1.0K   gbbct1.seq 2011-08-16 10:59 70K   gbest1.seq 2011-08-16 10:59 4.0K  …

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRef  CAS  PubMed  Google Scholar  Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database…

Barnett R. Schistosomiasis. (1474–547X (Electronic)). Steinmann P, Keiser J, Bos R, Tanner M, Utzinger J. Schistosomiasis and water resources development: systematic review, meta-analysis, and estimates of people at risk. Lancet Infect Dis. 2006;6(7):411–25. Article  PubMed  Google Scholar  Uthailak N, Adisakwattana P, Thiangtrongjit T, Limpanont Y, Chusongsang P, Chusongsang Y, et…

Adékambi T, Drancourt M, Raoult D (2009) The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 17:37–45 CrossRef  PubMed  Google Scholar  Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRef  CAS  PubMed  Google Scholar  Arahal DR,…

Tool:SEDA (SEquence DAtaset builder): a desktop tool for processing FASTA files containing DNA and protein sequences 4 Dear community members, We present SEDA, an open source application for processing FASTA files containing DNA and protein sequences. The source code is available at GitHub and a complete user manual is available…

The European Bioinformatics Institute (EMBL-EBI) offers a wide range of bioinformatics sequence analysis applications for free through web and programmatic access. This two-day course is designed to provide a comprehensive overview of sequence analysis tools and how to use the workflows effectively, covering hands-on exercises and demonstrations throughout.  The first…

It appears to me that the sam format used by emboss’s water disagrees with the Samtools spec for NM flag, which reads: NM: Number of differences (mismatches plus inserted and deleted bases) between the sequence and reference, counting only (case-insensitive) A, C, G and T bases in sequence and reference…

Blog:Perform Primer to Primer comparison to see and show if the primers produced are new or 100% similar to published primers 1 Hi Everyone I was recently asked to compare the primers we produced in our lab with the published primers and see if they are 100% similar or not….

Yang, Y. et al. Advances in the studies of plant diversity and ecological adaptation in the subnival ecosystem of the Qinghai-Tibet plateau. Chin. Sci. Bull. 64, 2856–2864 (2019). Article  Google Scholar  Zhang, Y., Li, B. & Zheng, D. Datasets of the boundary and area of the Tibetan plateau. Acta Geographica…

Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825–837 (2003). Article  ADS  CAS  PubMed  Google Scholar  Miga, K. H. et al. Centromere reference models for human chromosomes X and Y satellite arrays. Genome Res. 24, 697–707 (2014)….

Provided by: emboss_6.6.0+dfsg-11ubuntu1_amd64 NAME goseq – Identify sequence entries containing GO terms SYNOPSIS goseq -sequence seqall -term string -outfile outfile goseq -help DESCRIPTION goseq is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the “Edit” command group(s). OPTIONS Input section -sequence…

Highly degenerate primers and BLAST 0 Leray et al 2013‘s CO1 primers are commonly used in labs looking to detect vertebrates. I’ve been trying to include them in my in silico prep work but they’re so highly degenerate, I can’t get regular bioinformatics tools to work with them. The more…

O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion and functional annotation. Nucleic Acids Res. 44, D733–D745 (2016). Google Scholar  Frankish, A. et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 51, D942–D949 (2023). Google Scholar  Pertea,…

EMBOSS-FUZZNUC 0 Hello, I’m using EMBOSS for the first time and I have several doubts. I have got a short sequence of RNA. I need to find out if there is unintentional hybridisation with RNA regions similar to my sequence (Hybridisation-mediated off-targets). To do this what I have done is:…

Find the most similar regions of two dna sequences 1 I need to find the most similar regions of two DNA sequences. I already tried parallel alignment algorithms, but I don’t need to find the maximum alignments over the entire length of the sequences. I only need one longest possible…

Provided by: bioperl_1.7.7-1_all NAME bp_seqret – bioperl implementation of sequence fetch from local db (like EMBOSS seqret) USAGE bp_seqret [-f/–format outputformat] [-o/–out/–outfile outfile] [-d/–db dbname] [-i/–id/-s/–seqname seqname1] Example usage: bp_seqret -f fasta -db db.fa -i seq1 -i seq2 > output.fas bp_seqret db.fa:seq1 output.fas bp_seqret db.fa:seq1 -o output.fas bp_seqret -db db.fa…

Is it possible to get a pairwise distance matrix from a mafft alignment? 1 I’ve googled around a bit. From reading the publications and software documentation, its clear that there is a distance matrix being used but it doesnt seem possible to obtain. There is rumor of a –distout flag…

Provided by: emboss_6.6.0+dfsg-7ubuntu2_amd64 NAME cacheebeyesearch – Generates server cache file for EB-eye search domains SYNOPSIS cacheebeyesearch [-outfile outfile] -cachefile outfile cacheebeyesearch -help DESCRIPTION cacheebeyesearch is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the “Data resources” command group(s). OPTIONS Input section…

Are you looking for your next opportunity in bioinformatics? Then you need a strong CV that showcases your relevant qualifications and experience in the field. In this guide, we’ll teach you how to create an impressive application that showcases your top achievements. You can also check out our bioinformatics CV…

NLRP3 expression and purification Both wild-type NLRP3 and CAPS mutants were cloned in the mammalian expression vector pcDNA3.1HisB. Plasmid was purified using Qiagen Giga Prep up to 2000 ng/μl and subsequently transfected into Expi293 with Expifectamine per manufacturer instructions. Expression was allowed to proceed for 3 days before harvesting. Cells were…

How do i figure out whether a recognition site is conserved or not? 0 I have two sequences corresponding to the 16s rRNA gene for two strains of a certain species. I simulated the restriction digestion of these sequences using a restriction enzyme. How do i figure out if a…

tool that reports *every* ORF, including from nested starts? 2 (I am defining ORF as, between an ATG start and a downstream stop codon) Given a situation like this: showing a ~1kb region, forward strand, 3 frame prediction of starts (green) and stops (red), for the frame 3 span between…

Hi, How can I merge two paired end fastq (R and L) to give a single fastq file ? For information, the sequencing run is 72 bp long and it contains a majority of small RNA (miRNA,…) so a lot of paired end reads will overlap. For example here’s two…

Schmitz, J. F. & Bornberg-Bauer, E. Fact or fiction: updates on how protein-coding genes might emerge de novo from previously non-coding DNA. F1000Research 6, 57 (2017). Article  PubMed  PubMed Central  Google Scholar  Vakirlis, N. et al. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat. Commun. 11,…

Giovannoni, J. J. Genetic regulation of fruit development and ripening. Plant Cell 16, S170–S180 (2004). CAS  PubMed  PubMed Central  Google Scholar  Tieman, D. et al. A chemical genetic roadmap to improved tomato flavor. Science 355, 391–394 (2017). CAS  PubMed  Google Scholar  Peralta, I. E., Spooner, D. M. & Knapp, S….

Alignment REST API 1 Hello, I want to implement a rest api with python and requests to perform an alignment on Emboss needle www.ebi.ac.uk/Tools/psa/emboss_needle/ I have used the following code but I am getting the following error. I do not know what I’m doing wrong. Can somebody help me? Thank…

API REST ALINGMENT 1 Hello, I want to implement a rest api with python and requests to perform an alignment on Emboss needle www.ebi.ac.uk/Tools/psa/emboss_needle/ I have used the following code but I am getting the following error. I do not know what I’m doing wrong. Can somebody help me? Thank…

cacheebeyesearch(1) Generates server cache file for EB-eye search domains SYNOPSIS cacheebeyesearch [-outfile outfile] -cachefile outfile cacheebeyesearch -help DESCRIPTION cacheebeyesearch is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the “Data resources” command group(s). OPTIONS Input section Output section -outfile outfile Default value: stdout…

Stairs CW, Leger MM, Roger AJ. Diversity and origins of anaerobic metabolism in mitochondria and related organelles. Philos Trans R Soc B: Biol Sci. 2015;370:20140326. Article  Google Scholar  Eme L, Spang A, Lombard J, Stairs CW, Ettema TJG. Archaea and the origin of eukaryotes. Nat Rev Microbiol. 2017;15:711–23. Article  CAS …

core/ajrefseqdata.h Ajax refseq object. Holds the refseq itself, plus associated information. Alias name(s) Attributes Ajax refseq input object. Holds the input specification and information needed to read the refseq and possible further entries Alias name(s) Attributes Name Type Description Input AjPTextin General text input object RefseqData void* Format data for…

EMBOSS: dbxflat dbxflat   Function Index a flat file database using b+tree indices Description dbxflat indexes a flat file database of one or more files, and builds EMBOSS B+tree format index files. These indexes allow access of flat files larger than 2Gb. Usage Here is a sample session with dbxflat…

Biopython vs Python Hi, Please help – If already have python 3 in laptop, is biopython still needed to download? I already downloaded python 3; when I checked on the www.bippython.org, there is also “download”, are they the same or different? sorry if it is a naive question. Thank you…

Tool for aligning short protein sequences 2 Hi, I have a file that looks like: >ref_frame=1 XFKKNLAFLQKKAKEFSSEQTRANSPTRRELQVWGRDNNSPSEA >ref_frame=2 FLKKIWPSYKKRPKNFLQSRPEPTAPPEESFRSGVETTTPPQKQ >ref_frame=3 F*KKSGLPTKKGQRIFFRADQSQQPHQKRASGLG*RQQLPLRSR >read1_frame=1 FFKKNLAFLQKKAKEFSSEQTRANSPTRRELQVWGRDNNSPSEA >read1_frame=2 FLKKIWPSYKKRPKNFLQSRPEPTAPPEESFRSGVETTTPPQKQ >read1_frame=3 F*KKSGLPTKKGQRIFFRADQSQQPHQKRASGLG*RQQLPLRSR I want to do a protein alignment where I align each read frame against each ref frame. What tool can I use to…

Hi Maarten, This seems to stem from your latest upload of dssp. Could you consider taking a look at this one? Thanks, Nilesh On Sun, 1 Jan 2023 15:20:12 +0100 Lucas Nussbaum <lu…@debian.org> wrote: > Source: python-biopython > Version: 1.80+dfsg-4 > Severity: serious > Justification: FTBFS > Tags: bookworm sid ftbfs > User: lu…@debian.org > Usertags: ftbfs-20230101 ftbfs-bookworm > >…

HHS Vulnerability Disclosure, Help This document is an overview of the Entrez databases, with general information on If you are not sure that the “Save” option in your program will do this for you, use “Save As”, In Excel, select “Save As” from the File menu. optimizations to reduce memory…

The Job Dispatcher service at the EMBL-EBI provides access to various sequence analysis tools and a database retrieval system (Dbfetch). This virtual course is split into two sessions running over two days.  During the first session, you will learn how to access and use our sequence…

Experimental methods Stem cell and organoid culture We used six human iPS cell lines (Hoik1, Wibj2, Kucg2 from the HipSci resource47; 409B2 from the RIKEN BRC cell bank; 01F49i-N-B7 (B7) from Institute of Molecular and Clinical Ophthalmology Basel; and WTC from the Allen Institute) and three human ES cell lines (H1-PAX6YFP…

You really don’t need regular expressions for this. header = None length = 0 with open(‘file.fasta’) as fasta: for line in fasta: # Trim newline line = line.rstrip() if line.startswith(‘>’): # If we captured one before, print it now if header is not None: print(header, length) length = 0 header…

Serratus alignment architecture Serratus (v0.3.0) (github.com/ababaian/serratus) is an open-source cloud-infrastructure designed for ultra-high-throughput sequence alignment against a query sequence or pangenome (Extended Data Fig. 1). Serratus compute costs are dependent on search parameters (expanded discussion available: github.com/ababaian/serratus/wiki/pangenome_design). The nucleotide vertebrate viral pangenome search (bowtie2, database size: 79.8 MB) reached processing rates…

How to find the longest orf from a transcriptome 0 Hello, good day, sorry for the simplicity but, I have a super basic question. I have been trying to identify the longest ORF of a transcriptome for a long time, but from the previous failed attempts it seems that it…

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 –  …

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…

Remove Gaps from Multiple sequence alignment 2 I want to remove col that contains gaps in the MSA file… Any sort of python code that helps me??? col Remove in MSA • 28 views Not sure if it’s python code but I know that trimAL can be used for this….

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…

Hello all, Previously, I posted about a question in a similar vein (see here) BUT now, 2 weeks later, I think I am nearly there! I plan to update that previous post and explain what I’ve done once I’ve tackled this final bit. (TL;DR my other question: I used the…

Getting the same alignment from needle (emboss) and ggsearch36 0 I used to run ggsearch36 from the fasta package for NW alignment of proteins and now need to switch to needle from emboss, as ggsearch36 skips low-scoring alignments, whereas needle can return all. I’m looking for the correct configuration to…

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…

FYI, FreeBSD users can now install all the bioinformatics software referenced by the Biostar Handbook via FreeBSD ports. Everything except bedGraphToBigWig can be installed simply by running pkg install biostar-tools bedGraphToBigWig is part of ucsc-userapps, which cannot be redistributed for licensing reasons, so there is no binary package. However, the…

Hello all, Hope you’re well. I started a PhD in Jan this year and frankly I am struggling. I’m coming into the second week of trying to figure out how to attempt this problem and it’s honestly starting to get to me a bit – the current task I’m working…

Dnaman software manual DNADynamo DNA Sequence Analysis SoftwareCLC Genomics Workbench – Qiagen They have sent a man to locate the key. He was making notes with a slim gold pen on a Gucci pad? When I married my husband, that all…

EMBOSS transeq lines with “(REVERSE SENSE)” in not reverse sence translations(?) 0 Hi good day. Sorry, I have a silly doubt, if someone could help me I would really appreciate it. You see, I’m using EMBOSS’s transeq tool (something new for me) to translate an ORF file. When translating the…

Failed to open filename / unable to read – Ubuntu 1 Hii, i’ve been trying using primersearch from emboss on ubuntu but this keeps getting me the same error primersearch -seqall filename.fna -infile filename.txt -mismatchpercent 10 -outfile filename.primersearch Error: Failed to open filename ‘filename’ Error: Unable to read sequence ‘filename’…