Tag: SwissProt

UniProtKB/SwissProt variant VAR_013096

UniProtKB/SwissProt variant VAR_013096 Glycogen phosphorylase, liver form Gene: PYGL Feedback? Literature citations No reference for the current variant in UniProtKB/Swiss-Prot. Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as…

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hypothetical protein LOTGIDRAFT_99224 partial, maker-scaffold1322_size48131-snap-gene-0.13 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of hypothetical protein LOTGIDRAFT_99224 partial vs. L. salmonis genes Match: EMLSAG00000006769 (supercontig:LSalAtl2s:LSalAtl2s379:476161:478870:-1 gene:EMLSAG00000006769 transcript:EMLSAT00000006769 description:”maker-LSalAtl2s379-augustus-gene-4.10″) HSP 1 Score: 59.6918 bits (143), Expect = 4.225e-12Identity = 29/57 (50.88%), Postives = 39/57 (68.42%), Query Frame = 0 Query: 22 AANARERTRMRVLSKAFGRLKLTLPWVPPDTKLSKLDTLRLATSYISHLQRLLSDEE 78 +N +ER R + ++…

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How to avoid missannotated GO terms?

How to avoid missannotated GO terms? 1 Hi, I am doing GO enrichment analysis for the newly annotated plant genome. I did BLAST against Swissprot plant proteins and extracted the GO IDs of matching hits. I observed that there are some miss annotated proteins, like the following: P04145 (Assigned GO…

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Reducing variability in protein purification

In this article, Analytik Jena details what technology can make protein purification less variable and faster with the help of liquid-handling equipment. The CyBio FeliX and PhyTips® can conduct 96 targeted protein purifications in 120 minutes, requiring no hands-on time. These products are intended for drug discovery professionals in the…

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The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids

Genome sequencing and assembly of R. tetraphylla After DNA extraction from young leaves and sequencing, the R. tetraphylla genome was first assembled into 1008 contigs with an N50 of 3.7 Mb. After haplotigs removal and a final pilon polishing, the 364,945,498 bp final assembly was distributed across 76 scaffolds with an N50…

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30ul | Anti-SMAD4 Antibody Clinisciences

Description: Rabbit polyclonal antibody to SMAD4 Immunogen: KLH-conjugated synthetic peptide encompassing a sequence within the N-term region of human SMAD4. The exact sequence is proprietary. Purification: The antibody was purified by immunogen affinity chromatography. Clonality: Polyclonal Form: Liquid in 0.42% Potassium phosphate, 0.87% Sodium chloride, pH 7.3, 30% glycerol, and…

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Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis

Identification of CH cases from WGS in ISL and UKB We used WGS from 45,510 Icelanders and 130,709 British ancestry participants from the UKB17,18. Average sequencing depth was 33× for UKB and 38× for ISL. Participants with prior diagnoses of hematological disorders or grossly abnormal hematology measurements on entry were…

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Solved Part 2: UniProtKB/SwissProt and Protein Data Bank

Transcribed image text: Part 2: UniProtKB/SwissProt and Protein Data Bank Analysis on SARS-CoV-2 Non-Structural Proteins Objective: Explore the structures, functions, and interactions of SARS-CoV-2 non-structural proteins using resources from UniProtKB/SwissProt and the Protein Data Bank, 1) Visit the PDB resource on SARS-CoV-2 proteins and select a non-structural protein (e.g., NSP3,…

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Practical 6 Final 320 GENE – GENE 320 Practical 6 Advanced BLAST Start with a brief introduction

GENE 320 Practical 6 Advanced BLAST Start with a brief introduction [150 words] and aim of the practical. [5] An Introduction should have relevant information relating to the practical, including at least 2 in-text citations from scientific literature (3 marks). The aim/s should be clearly stated. (2 mark) The aim…

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python – retrieving past BLAST requests in bioPython

python – retrieving past BLAST requests in bioPython – Bioinformatics Stack Exchange …

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papain family cysteine protease containing protein, maker-scaffold1702_size30647-snap-gene-0.14 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of papain family cysteine protease containing protein vs. L. salmonis genes Match: EMLSAG00000006045 (supercontig:LSalAtl2s:LSalAtl2s327:400616:404607:-1 gene:EMLSAG00000006045 transcript:EMLSAT00000006045 description:”augustus_masked-LSalAtl2s327-processed-gene-4.0″) HSP 1 Score: 590.497 bits (1521), Expect = 0.000e+0Identity = 283/525 (53.90%), Postives = 368/525 (70.10%), Query Frame = 0 Query: 49 GHVARPLGKSPPNFVRDPPPRTTPPAQWLWNNVNETNFLTVSRNQHLPTYCGSCWAHAATSSLSDRIKIARQGAWPDINLAPQVLISCGPGDGCHGGEAGDANAYMHAQGITDETCSIYRARGQDNGLPCSKLEICSTCE—SKCYQPQHFFTYRVDEFHDVEGESNGEQEANMMAEIHHRGPISCGIAVTQALV-NYTGGLFHDKTGAQEIDHDISVVGYGVDEGTQEKYWLIRNSWGTYWGEQGFFRLIRGVNNLGIESGTCSWATPADTWSDAARE—RAAILSNEITLQKP——LWKQLWTVVADFVDNTRDTDLFRRLKLMQKGCKKLSSPRVPVVNIRPRPQDYVSTADLPEALDWRSVNGTNFLSWSVNQHLPVYCGSCWAQAGLSSLADRFTIADRKRFANLALSVQYILNCQAGGSCHGGDAFPLYAFIQKQGVPDVTCQPYEALDEGPLTDCSKPSKLVCKDCTWPPPEPGQEGNCWAKEKFHRYYVDEYNGVEGADNMKKEILERGPVT 560 GH+ R G+…

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coatomer subunit alpha, maker-scaffold52_size450388-snap-gene-3.16 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of coatomer subunit alpha vs. L. salmonis genes Match: EMLSAG00000004199 (supercontig:LSalAtl2s:LSalAtl2s221:488387:561813:1 gene:EMLSAG00000004199 transcript:EMLSAT00000004199 description:”maker-LSalAtl2s221-augustus-gene-5.19″) HSP 1 Score: 208.379 bits (529), Expect = 8.743e-63Identity = 95/135 (70.37%), Postives = 99/135 (73.33%), Query Frame = 0 Query: 1 MLTKFETKSPRVKGLAFHPQRPWILASLHNGVIQLWDYRMCTLLEKFDEHEGPVRGIGFHAQQPLFVSGGDDYKIKVWNYKLKRCLFHLLGHLDYIRTTVFHAPVPHARRISPAGPAESSTYLAKIHGLWGWKAR 135 MLTKFETKSPRVKGLAFHP+RPWILASLHNGVIQLWDYRMC LLEKFDEHEGP GI H QPLFVSGGDDYKIKVWNYKLKRCLF LLGHLDYIR…

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Tools : SwissProt keywords results

References : Al-Shahrour, F., Minguez, P., Tárraga, J., Montaner, D., Alloza, E., Vaquerizas, J.MM., Conde, L., Blaschke, C., Vera, J. & Dopazo, J. (2006), BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments, Nucleic Acids Research, In Press, Al-Shahrour, F., Minguez, P., Vaquerizas, J.M., Conde, L. &…

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Assistance with Fungal Genome Annotation Using Maker and BLAST

Hello everyone, I’m a new user of Maker and I’m seeking assistance with the protocol I’m using. Currently, I’m working on annotating the genome of a non-model ascomycete fungal species belonging to the Sporocadaceae family. After running the analysis with Maker, I obtained FASTA and GFF files using fasta_merge and…

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Clustering-predicted structures at the scale of the known protein universe

Structural clustering algorithm The clustering procedure is similar to MMseqs2’s clustering but, instead of using sequences, Foldseek’s 3Di alphabet (Extended Data Fig. 1) was used to represent the structures as one-dimensional sequences. The clustering algorithm combines Linclust17 and cascaded MMseqs2 (ref. 42) clustering. The pipeline applies this strategy to allow for efficient…

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hypothetical protein LOTGIDRAFT_112989, maker-scaffold299_size217019-snap-gene-1.29 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of hypothetical protein LOTGIDRAFT_112989 vs. L. salmonis genes Match: EMLSAG00000011196 (supercontig:LSalAtl2s:LSalAtl2s761:366436:368626:1 gene:EMLSAG00000011196 transcript:EMLSAT00000011196 description:”maker-LSalAtl2s761-augustus-gene-2.9″) HSP 1 Score: 208.764 bits (530), Expect = 1.424e-65Identity = 100/171 (58.48%), Postives = 126/171 (73.68%), Query Frame = 0 Query: 120 NPIVFFDITIGGDPVGRIVMELYANVVPKTVDNFRALCTGEKGQVGGSGIPLHYKNSSFHRVINRFMLQGGDFTAGDGTGGASIYGEKFADENFLLKHEKPGLLSMANAGPGTNGSQFFLTTVNCPHLDGKHVVFGRAIKGMGIVNEIEVMETT-SDKPNVEVKIADCGQI 289 NP+VFFDI +G +GRIVMEL+A+V PKT +NFR CTGE…

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UniProtKB/SwissProt variant VAR_086765

UniProtKB/SwissProt variant VAR_086765 Dolichyl-diphosphooligosaccharide–protein glycosyltransferase subunit STT3A Gene: STT3A Feedback? Literature citations Active site variants in STT3A cause a dominant type I congenital disorder of glycosylation with neuromusculoskeletal findings. Wilson M.P.; Garanto A.; Pinto e Vairo F.; Ng B.G.; Ranatunga W.K.; Ventouratou M.; Baerenfaenger M.; Huijben K.; Thiel C.; Ashikov…

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Functional annotation of BRAKER output

Functional annotation of BRAKER output 0 I’m trying to do a functional annotation of a BRAKER’s output. I didn’t find any scripts inside BRAKER so I’m using maker_functional_fasta. However, using this: !maker_functional_fasta $insect_swissprot $blast_out.blastp $path_to_proteins > $proteins_with_headers gives this error: Use of uninitialized value $mol_type in concatenation (.) or string…

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blastp: parameter set

blastp: parameter set 0 Hi, I am new at bioinforamtic world. I am looking for homology of my target sequences through blastp with Swissport database. My subjects and querry bothfiles are large and expecting a large number of hits as well. Currently, I am running the code- blastp -query pep.fasta…

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UniProtKB/SwissProt variant VAR_086244

UniProtKB/SwissProt variant VAR_086244 Atrial natriuretic peptide receptor 3 Gene: NPR3 Feedback? Literature citations Bi-allelic Loss-of-Function Mutations in the NPR-C Receptor Result in Enhanced Growth and Connective Tissue Abnormalities. Boudin E.; de Jong T.R.; Prickett T.C.R.; Lapauw B.; Toye K.; Van Hoof V.; Luyckx I.; Verstraeten A.; Heymans H.S.A.; Dulfer E.;…

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UniProtKB/SwissProt variant VAR_084861

UniProtKB/SwissProt variant VAR_084861 Retinal-specific phospholipid-transporting ATPase ABCA4 Gene: ABCA4 Feedback? Literature citations Novel mutations in of the ABCR gene in Italian patients with Stargardt disease. Passerini I.; Sodi A.; Giambene B.; Mariottini A.; Menchini U.; Torricelli F.; Eye 24:158-164(2010) Cited for: VARIANTS STGD1 21-GLN–ASP-2273 DEL; LEU-68; HIS-96; LYS-96; SER-172; CYS-212;…

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UniProtKB/SwissProt variant VAR_086367

UniProtKB/SwissProt variant VAR_086367 Transportin-2 Gene: TNPO2 Feedback? Literature citations TNPO2 variants associate with human developmental delays, neurologic deficits, and dysmorphic features and alter TNPO2 activity in Drosophila. Goodman L.D.; Cope H.; Nil Z.; Ravenscroft T.A.; Charng W.L.; Lu S.; Tien A.C.; Pfundt R.; Koolen D.A.; Haaxma C.A.; Veenstra-Knol H.E.; Wassink-Ruiter…

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UniProtKB/SwissProt variant VAR_086225

UniProtKB/SwissProt variant VAR_086225 H(+)/Cl(-) exchange transporter 3 Gene: CLCN3 Feedback? Literature citations Unique variants in CLCN3, encoding an endosomal anion/proton exchanger, underlie a spectrum of neurodevelopmental disorders. Duncan A.R.; Polovitskaya M.M.; Gaitan-Penas H.; Bertelli S.; VanNoy G.E.; Grant P.E.; O’Donnell-Luria A.; Valivullah Z.; Lovgren A.K.; England E.M.; Agolini E.; Madden…

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PROTEIN & MORE – Cutiswiss

PROTEIN & MORE – Cutiswiss Buy Skin Care products suited for you at best prices in India Home PROTEIN & MORE Showing 1–15 of 16 results Cutiswiss Swissprot Senior’s Protein 1 kg. Rs.1,899.00 Cutiswiss Swissprot Pure Creatine Monohydrate 300 gm. Rs.2,999.00 Cutiswiss Swissprot Women’s Protein 360 gm. Rs.999.00 cutiswiss Swissprot…

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DeepMind AI Powers Major Scientific Breakthrough: AlphaFold Generates 3D View of the Protein Universe

AlphaFold predicts the structure of almost every cataloged protein known to science. Credit: Karen Arnott/EMBL-EBI AI-powered predictions of the three-dimensional structures of nearly all cataloged proteins known to science have been made by DeepMind and EMBL’s European Bioinformatics Institute (EMBL-EBI). The catalog isfreely and openly available to the scientific community,…

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UniProtKB/SwissProt variant VAR_087010

DNA ligase 1 Gene: LIG1 Feedback? Literature citations Biallelic mutations in DNA ligase 1 underlie a spectrum of immune deficiencies. Maffucci P.; Chavez J.; Jurkiw T.J.; O’Brien P.J.; Abbott J.K.; Reynolds P.R.; Worth A.; Notarangelo L.D.; Felgentreff K.; Cortes P.; Boisson B.; Radigan L.; Cobat A.; Dinakar C.; Ehlayel M.;…

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UniProtKB/SwissProt variant VAR_085880

60S ribosomal protein L3-like Gene: RPL3L Feedback? Literature citations Bi-allelic missense disease-causing variants in RPL3L associate neonatal dilated cardiomyopathy with muscle-specific ribosome biogenesis. Ganapathi M.; Argyriou L.; Martinez-Azorin F.; Morlot S.; Yigit G.; Lee T.M.; Auber B.; von Gise A.; Petrey D.S.; Thiele H.; Cyganek L.; Sabater-Molina M.; Ahimaz P.;…

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UniProtKB/SwissProt variant VAR_086574

Mothers against decapentaplegic homolog 2 Gene: SMAD2 Feedback? Literature citations De novo mutations in histone-modifying genes in congenital heart disease. Zaidi S.; Choi M.; Wakimoto H.; Ma L.; Jiang J.; Overton J.D.; Romano-Adesman A.; Bjornson R.D.; Breitbart R.E.; Brown K.K.; Carriero N.J.; Cheung Y.H.; Deanfield J.; DePalma S.; Fakhro K.A.;…

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Chromosome-level genome assemblies from two sandalwood species provide insights into the evolution of the Santalales

Genome sequencing and assembly We sequenced and assembled genomes for the sandalwood species S. album and S. yasi (Fig. 1). In total, ~23 Gb and ~25 Gb of clean short reads of S. album and S. yasi were obtained for the genomic survey, respectively (Supplementary Tables 1 and 2). According to k-mer analysis, the…

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protein abrupt-like isoform x1, maker-scaffold97_size377342-snap-gene-2.14 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of protein abrupt-like isoform x1 vs. L. salmonis genes Match: EMLSAG00000011120 (supercontig:LSalAtl2s:LSalAtl2s753:207020:208693:1 gene:EMLSAG00000011120 transcript:EMLSAT00000011120 description:”augustus_masked-LSalAtl2s753-processed-gene-1.1″) HSP 1 Score: 342.043 bits (876), Expect = 1.286e-109Identity = 269/559 (48.12%), Postives = 311/559 (55.64%), Query Frame = 0 Query: 168 DNFGPSAPKRHRFNGPESRNSPSSSPKSLADWGRRSLEPKTEDTAEADNNNSTPKSESLLSQALEKHSNVSSMYDRHLLRDNGDGRDGDSASDTTSERPESLMDGLIKNSGAESELHRQLSAASPASMGGHLFPPGLEALYRQAGFPSAFLGLAAGAA—-GGSPGG————–PVSSMHGLASSVPQVGLQSHAGNPN—————————————–LAGKLDMMRVRATDPRPCPKCGKIYRSAHTLRTHMEDKHTICPGYRCVLCGTVAKSRNSLHSHMSRQHRGISTKDLPVLPMPSPFDPALASRLLAKAGVKVTPNELAARASPTAPRRSDLPKLDTNLLHM-HHHQFPLPPSLPT-SMSGHMGRGSHDGNGSDVEDLRVSSAPSPFGSNGGPGGIYSQAHQMRIAQGMLSPKDFA–ALASAGGAQGAAGMGSALLDTYLSMI-AAAGGDSNPMAAALNFQ-NPASRAAAFAAAAAAASGNQAHNGDGKDNDQRSGVSEDRDDMTGELGSDADNDDLSDNDD 661 D++ P PKRHR NG E…

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Prediction of protein subplastid localization and origin with PlastoGram

Data sets To create data sets of sequences corresponding to compartments of photosynthetic plastids, we searched the UniProt database for proteins annotated as localized in the chloroplast. Importantly, the UniProt keyword ’Chloroplast’ includes not only chloroplasts of green algae and land plants but also plastids of Rhodophyta, haptophytes and the…

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Splitting of VCF file of CSQ field in the INFO column to tabular format.

VCF file will be having seven fixed columns and INFO column. Chromosome, position, ID, ref, alt, qual, filter, and INFO column. This INFO column will be having the variant related information. In the INFO column CSQ field will be having multiple fields – 82 fields fixed with the delimeter “|”…

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Ubuntu Manpage: Bio::DB::Flat::BDB::swiss – swissprot adaptor for Open-bio standard BDB-indexed flat file

Provided by: libbio-perl-perl_1.6.924-3_all NAME Bio::DB::Flat::BDB::swiss – swissprot adaptor for Open-bio standard BDB-indexed flat file SYNOPSIS See Bio::DB::Flat. DESCRIPTION This module allows swissprot files to be stored in Berkeley DB flat files using the Open- Bio standard BDB-indexed flat file scheme. You should not be using this directly, but instead use…

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NCBI Blast databases – cannot find some databases

NCBI Blast databases – cannot find some databases – Bioinformatics Stack Exchange …

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I need to define a ground truth/correct answer set of GO terms for proteins

I need to compare the predictions of a GO term prediction method, across some dataset. How do I go about creating the test dataset? I want each protein in dataset to have the ground truth/correct answers GO terms, so that I can compare the ‘correct’ answer to the predictions generated…

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NCBI BLAST+ 2.14.0 release includes faster protein and translation search options

News:NCBI BLAST+ 2.14.0 release includes faster protein and translation search options 0 Protein and translated DNA (BLASTP, BLASTX, and TBLASTN) BLAST searches are now faster with the inclusion of support for initial long words. This improvement speeds up the fast modes, -task blastp-fast, -task blastx-fast, -task tblastn-fast on the command-line….

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Solved AssignmentUsing the generic Python template below,

Assignment Using the generic Python template below, write a script called addKEGGPathways.py to do the following: Filter to only BLAST output where evalue < 1e-50 Append the KEGG Ortholog ID, KEGG Pathway ID, and KEGG Pathway Description for each of the SwissProt (Uniprot) IDs Skip PathIDs that start with ‘path:map’…

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AssignmentUsing the generic Python template below,

Assignment Using the generic Python template below, write a script called addKEGGPathways.py to do the following: Filter to only BLAST output where evalue < 1e-50 Append the KEGG Ortholog ID, KEGG Pathway ID, and KEGG Pathway Description for each of the SwissProt (Uniprot) IDs Skip PathIDs that start with ‘path:map’…

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UniProtKB/SwissProt variant VAR_031448

Ribonuclease SLFN12Gene: SLFN12 Variant information Variant position:  168 The position of the amino-acid change on the UniProtKB canonical protein sequence. Type of variant:  LB/B The variants are classified into three categories: LP/P, LB/B and US. LP/P: likely pathogenic or pathogenic. LB/B: likely benign or benign. US: uncertain significance Residue change:  From Cysteine (C)…

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UniProtKB/SwissProt variant VAR_086203

Sequence information Variant position:  384 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  788 The length of the canonical sequence. Location on the sequence:   LGVSGASLGVPLEEEEGLLS  S HWEARLLQGSLMTATFDGAQ The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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Salamandra salamandra homology annotation blastp-swissprot

Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Mounting evidence is showing that attitude to disperse is unevenly distributed among individuals within animal populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here,…

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ISC Class 12 Biotechnology Syllabus 2022

ISC Class 12th Biotechnology Syllabus 2023: Biotechnology is a field of science that applies biological processes, organisms, or systems to develop products or technologies that improve human lives. It involves using living organisms or their derivatives to create new products or processes. Biotechnology has multiple applications in various areas such…

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CPU usage limit was exceeded, resulting in SIGXCPU (24) on remote blastp search

Error: CPU usage limit was exceeded, resulting in SIGXCPU (24) on remote blastp search 0 I have been attempting to use command line blastp to search amino acid sequences from a transcriptome. I started with 34 sequences in the fasta, and got the error: Error: CPU usage limit was exceeded,…

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nadh dehydrogenase subunit 1, maker-scaffold1053_size66761-snap-gene-0.11 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of nadh dehydrogenase subunit 1 vs. SwissProt Match: gi|7994638|sp|O78701.1|NU1M_BRAVA (RecName: Full=NADH-ubiquinone oxidoreductase chain 1; AltName: Full=NADH dehydrogenase subunit 1) HSP 1 Score: 117.472 bits (293), Expect = 1.963e-31Identity = 62/128 (48.44%), Postives = 86/128 (67.19%), Query Frame = 0 Query: 1 MVGALRGIAQTISYEISLSLLILSLAFSVRTFSLADLSGHLARCPIYALTAPLVALWLVSCIAETNRTPFDFAEGESELVSGFNVEYGGFMFALIYMAEYGIILYFSILTTSLFF——-FPALET 121 ++GALR…

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Anti-Smad4 antibody KO Tested (ab110175)

Overview Product name Description Rabbit polyclonal to Smad4 Host species Rabbit Tested applications Species reactivity Reacts with: HumanPredicted to work with: Mouse, Rat, Sheep, Horse, Cow, Dog, Pig, Chimpanzee,…

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UniProtKB/SwissProt variant VAR_086837

Sequence information Variant position:  156 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  337 The length of the canonical sequence. Location on the sequence:   LNRTLSKLQWVSVFMLCAGV  T LVQWKPAQATKVVVEQNPLL The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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Solved 3.Run a standard protein-protein BLAST of the globin

3.Run a standard protein-protein BLAST of the globin sequence GLB5_PETMA against the SWISSPROT database; write down the number of hits and the E value of the least significant hit. Now run PSI-Blast with the same sequence; write down the number of hits and E value of the least significant hit…

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More up-regulated genes annotate to known GO/KEGG than down-regulated genes

More up-regulated genes annotate to known GO/KEGG than down-regulated genes 0 Hello, I have a dataset of RNA-seq data where I needed to do a de novo assembly. I am curious if anyone has any ideas why my dataset has an overrepresentation of DOWN regulated genes when I calculate DEGs…

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Which AF column do I use from TCGA data in maftools

Which AF column do I use from TCGA data in maftools 0 Currently trying to read a maf file from the TCGA and need to change the headers in order to run it but not sure what column in the TCGA file corresponds to the ‘i_TumorVAF_WU’ header I need. Below…

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RNAseq-derived Read Counts for Primary and Locally Recurring Breast Cancers

Read counts from RNAseq analysis for all 75 breast cancer samples included in the study “Proteogenomics decodes the evolution of human ipsilateral breast cancer”. De Marchi T, Pyl PT, Sjöström M, Reinsbach SE, DiLorenzo S, Nystedt B, Tran L, Pekar G, Wärnberg F, Fredriksson I, Malmström P, Fernö M, Malmström…

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Neuropeptide S receptor (Npsr1), Recombinant Protein | Protein/peptide search engine | Protein search engine

Name Neuropeptide S receptor (Npsr1), Recombinant Protein Supplier MyBioSource Catalog MBS7023446 Category Protein Prices $1,180.00, $2,165.00, $3,375.00 Sizes 10 µg, 50 µg, 100 µg Species Reactivities Rat Nature Recombinant Source Cell Free Expression Tag/Conjugation Tag type will be determined during the manufa SwissProt/Accession P0C0L6 Gene Npsr1 Sequence MPANLTEGSF HANQTVPMLD SSPVACTEIV…

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Availability of information on genes in Gnomad VCF data

Availability of information on genes in Gnomad VCF data 1 Hi , Im new to gnomad and genetics in general and i was wondering does the gnomad genome data that is downlaoded in the vcf format on variants contains information of what is the nearest gene and is the genomic…

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UCSC Genome Browser | Encyclopedia MDPI

1. History Initially built and still managed by Jim Kent, then a graduate student, and David Haussler, professor of Computer Science (now Biomolecular Engineering) at the University of California, Santa Cruz in 2000, the UCSC Genome Browser began as a resource for the distribution of the initial fruits of the…

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Index of /~psgendb/birchhomedir/public_html/doc/local/biopython-1.55.old/Tests/SwissProt

Name Last modified Size Description Parent Directory   –   keywlist.txt 2010-10-07 10:28 3.2K   keywlist2.txt 2010-10-07 10:28 1.3K   sp001 2010-10-07 10:28 3.2K   sp002 2010-10-07 10:28 2.7K   sp003 2010-10-07 10:28 6.9K   sp004 2010-10-07 10:28 4.7K   sp005 2010-10-07 10:28 2.3K   sp006 2010-10-07 10:28 2.4K  …

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How To Install libbio-db-swissprot-perl on Kali Linux

In this tutorial we learn how to install libbio-db-swissprot-perl on Kali Linux. libbio-db-swissprot-perl is Database object interface to SwissProt retrieval Introduction In this tutorial we learn how to install libbio-db-swissprot-perl on Kali Linux. What is libbio-db-swissprot-perl SwissProt is a curated database of proteins managed by the Swiss Bioinformatics Institute. Additional…

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Issues with searching Swissprot #25

Eddykay310 Hi @cruizperez Please help me understand the problem here and how I can fix it. I have successfully generated my DBs but I get this error during analysis. The .dmnd files do not exist in the folders as the error says but I don’t know how I can generate…

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Using Biopython to Retrieve Isoform Sequences of a Swissprot Entry?

You could use the Proteins API of EBML-EBI and a few lines of Python code. This will give you only the sequence as a string, not as a fully fledged BioPython object. import requests import xml.etree.ElementTree as ET accession = “Q16620” # a dictionary storing the sequence of your isoforms,…

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UniProtKB/SwissProt variant VAR_083844

Sequence information Variant position:  755 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  1473 The length of the canonical sequence. Location on the sequence:   MAHFEEMGMCVETDMELLVC  T FCIKFSRHVKKLQLIEGRQH The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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UniProtKB/SwissProt variant VAR_082091

Sequence information Variant position:  575 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  749 The length of the canonical sequence. Location on the sequence:   NLPYPLILRPQRGVDLIISF  D FSARPSDSSPPFKELLLAEK The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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UniProtKB/SwissProt variant VAR_075821

Sequence information Variant position:  340 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  418 The length of the canonical sequence. Location on the sequence:   NFAASLCSDVILYPLETVLH  R LHIQGTRTIIDNTDLGYEVL The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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UniProtKB/SwissProt variant VAR_082102

Sequence information Variant position:  507 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  1247 The length of the canonical sequence. Location on the sequence:   PPPSQPDPEHLDKPKLKAGG  S VESLRSSLSGQSSMSGQTVS The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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UniProtKB/SwissProt variant VAR_081147

Sequence information Variant position:  95 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  290 The length of the canonical sequence. Location on the sequence:   KLRQPFFQKRSELIAKIPNF  W VTTFVNHPQVSALLGEEDEE The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

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UniProtKB/SwissProt variant VAR_030440

Sequence information Variant position:  733 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  1333 The length of the canonical sequence. Location on the sequence:   RMEEFIGTVRGKAMKKWVES  I TKIIQRKKIARDNGPGHNIT The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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peroxisomal multifunctional enzyme type 2-like, maker-scaffold366_size194251-snap-gene-0.19 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of peroxisomal multifunctional enzyme type 2-like vs. L. salmonis genes Match: EMLSAG00000010112 (supercontig:LSalAtl2s:LSalAtl2s668:190059:194758:1 gene:EMLSAG00000010112 transcript:EMLSAT00000010112 description:”augustus_masked-LSalAtl2s668-processed-gene-1.1″) HSP 1 Score: 102.064 bits (253), Expect = 2.195e-25Identity = 65/191 (34.03%), Postives = 101/191 (52.88%), Query Frame = 0 Query: 134 GKVALVTGAGGGLGKAYALLLASRGASVVVNDLGGSRTGEGQSSKAADEVVNEIRQKGGKAV—–GNYDSVEDGEAVIKTALDNFGRIDIVINNAGILRDRSIGRTSDSDWDLVQKVHLRGAFQVIRAAWPHMKKQKYGRIINTSSVAGIFGNFGQSNYSSAKAGLIGLTSTLAIEGERSGIQANVIVP 319 GKVAL+TGA G+G++ A+L A…

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UniProtKB/SwissProt variant VAR_081813

Sequence information Variant position:  28 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  230 The length of the canonical sequence. Location on the sequence:   ILLFVTELSGAHNTTVFQGV  A GQSLQVSCPYDSMKHWGRRK The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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UniProtKB/SwissProt variant VAR_081661

Sequence information Variant position:  28 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  311 The length of the canonical sequence. Location on the sequence:   RALAAAAPASGKAKLTHPGK  A ILAGGLAGGIEICITFPTEY The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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Rat Anti-Mouse CD25/IL-2R Antibody

Name Rat Anti-Mouse CD25/IL-2R Antibody (GWB-31929F) Related Product Names Rat Anti-Mouse CD25/IL-2Ra-PE; PMP-22; Protein CD25; SR13 myelin protein; Schwann cell membrane glycoprotein; SAG Cd25; Pmp-22Rat Anti-Mouse CD25/IL-2RPmp22 Gene Symbol IL2RA Gene Fullname Interleukin-2 receptor subunit alpha Gene id 3559 Swissprot ID P01589 Protein Name Interleukin-2 receptor subunit alpha Protein Accession…

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UniProtKB/SwissProt variant VAR_081680

Sequence information Variant position:  126 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  230 The length of the canonical sequence. Location on the sequence:   GLYQCQSLHGSEADTLRKVL  V EVLADPLDHRDAGDLWFPGE The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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UniProtKB/SwissProt variant VAR_082098

Sequence information Variant position:  729 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  1053 The length of the canonical sequence. Location on the sequence:   CELCVKSFVTKRSLQEHMSI  H TGESKYLCSVCGKSFHRGSG The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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UniProtKB/SwissProt variant VAR_085098

Sequence information Variant position:  322 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  360 The length of the canonical sequence. Location on the sequence:   IEVEQALAHPYLEQYYDPSD  E PIAEAPFKFDMELDDLPKEK The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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UniProtKB/SwissProt variant VAR_083726

Sequence information Variant position:  468 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  805 The length of the canonical sequence. Location on the sequence:   GTLPFTYMLEKWRWMVFKGE  I PKDQWMKKWWEMKREIVGVV The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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UniProtKB/SwissProt variant VAR_084538

Sequence information Variant position:  28 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  492 The length of the canonical sequence. Location on the sequence:   PPAIGPYYENHGYQPENPYP  A QPTVVPTVYEVHPAQYYPSP The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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UniProtKB/SwissProt variant VAR_084474

Sequence information Variant position:  205 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  496 The length of the canonical sequence. Location on the sequence:   ERSLDTLLEAVESRGGVPGG  C VLVPRADLRLGGQPAPPQLL The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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UniProtKB/SwissProt variant VAR_082259

Sequence information Variant position:  4075 The position of the amino-acid change on the UniProtKB canonical protein sequence. Protein sequence length:  4374 The length of the canonical sequence. Location on the sequence:   GQDAGGLLREWYMIISREMF  N PMYALFRTSPGDRVTYTINP The residue change on the sequence. Unless the variant is located at the beginning or at the end of…

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hypothetical protein DAPPUDRAFT_213302, maker-scaffold2255_size18018-snap-gene-0.6 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of hypothetical protein DAPPUDRAFT_213302 vs. L. salmonis genes Match: EMLSAG00000000401 (supercontig:LSalAtl2s:LSalAtl2s1063:86108:87342:-1 gene:EMLSAG00000000401 transcript:EMLSAT00000000401 description:”maker-LSalAtl2s1063-snap-gene-0.46″) HSP 1 Score: 149.443 bits (376), Expect = 4.121e-44Identity = 91/196 (46.43%), Postives = 119/196 (60.71%), Query Frame = 0 Query: 14 MDKITDLQVEPLT–NSRFVKPLRLRFKQDGKVKVWDLIQCHASVAVVIFNQTTQKFVFVRQFRPAVYFSALRRAQGDVEPGTQFKGDEIDPKVGITLELCAGIVD-KSKSLIEIAHEEILEETGYDVPMNLIEEIQTFPVGVGVGGENMTLFCAEVTEAMRKGPGGGLAEEGEMIDVIEMGVEETRTLMRAKSVT 206 MDK+ VEPL +SRFV P R+ ++Q+G…

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Biopython Contact Map | Contact Information Finder

Listing Results Biopython Contact Map Protein Contact Maps using Biopython Warwick 9 hours ago Warwick.ac.uk View All Protein Contact Maps using Biopython. When working with protein 3D structures, a contact map is usually defined as a binary matrix with the rows and columns representing the residues of two different chains….

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BLASTP version 4 database error *Help

I am having trouble running the blastp command. When I run this command against the Swiss-prot database installed from the NCBI i get this error $ blastp -db swissprot -query Ecoli_rpoB.fasta -out TEST15.txt BLAST Database error: Error: Not a valid version 4 database. However, when I create my own database…

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probable dimethyladenosine transferase-like, maker-scaffold153_size302544-snap-gene-2.18 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of probable dimethyladenosine transferase-like vs. L. salmonis genes Match: EMLSAG00000006273 (supercontig:LSalAtl2s:LSalAtl2s341:673186:674124:1 gene:EMLSAG00000006273 transcript:EMLSAT00000006273 description:”augustus_masked-LSalAtl2s341-processed-gene-6.3″) HSP 1 Score: 484.567 bits (1246), Expect = 2.083e-174Identity = 227/310 (73.23%), Postives = 259/310 (83.55%), Query Frame = 0 Query: 9 KVRKTGSGMSTVEAAGSGGGGQQGMVFNTGLGQHILKNPLVVQSIIDKAALRSTDVVLEIGPGTGNLTVRALEKCKKLIACEVDPRMVAELQKRVQGTHFQSKLQIMVGDVIKTDLPFFDACVANVPYQISSPLVFKLLLHRPFFRCAVLMFQREFAQRLVAKPGDKLYCRLSINTQLLARVDHVMKVGKGNFRPPPKVESSVVRIEPRNPPPPINFKEWDGLTRVAFVRKNKTLGAAFNQTTVLMMLEKNYRVHLSLADEPVPEKIDIKSIIETVLAEIAFKEKRARSMDIDDFMKLLHAFNAKGIHFV 318 KV+ T + GG+QG+VFNT LGQHILKNP VV…

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How To Use Python Retrieve Results From Uniprot Automatically

How To Use Python Retrieve Results From Uniprot Automatically 3 You can use this: wget –quiet -O- ftp.uniprot.org/pub/databases/uniprot/currentrelease/knowledgebase/complete/uniprotsprot.dat.gz | zcat | python uniprot2go.py GO:0070337 GO:0016021 > out.fasta #!/usr/bin/env python “””Fetch uniprot entries for given go terms””” import sys from Bio import SwissProt #load go terms gos = set(sys.argv[1:]) sys.stderr.write(“Looking for…

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