Tag: UniProtKB

EMDB < EMD-20433

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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Ensembl ID mapping GRCh37 vs GRCh38

Ensembl ID mapping GRCh37 vs GRCh38 0 I currently have a large list of Ensembl protein IDs (ENSP) that are from GRCh37. I need to map these IDs to the entry name listed on the UniProt website (e.g. ‘CASPE_HUMAN’ ). I am having trouble doing this using the UniProt dataset…

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EnWik > Expasy

Expasy is an online bioinformatics resource operated by the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools and supports a range of life science and clinical research areas, from genomics, proteomics and structural biology, to evolution…

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UniProt: A0A6I9ZUN5_ACIJB

ID A0A6I9ZUN5_ACIJB Unreviewed; 234 AA. AC A0A6I9ZUN5; DT 07-OCT-2020, integrated into UniProtKB/TrEMBL. DT 07-OCT-2020, sequence version 1. DT 25-MAY-2022, entry version 6. DE SubName: Full=tumor necrosis factor ligand superfamily member 8 {ECO:0000313|RefSeq:XP_014931799.1}; GN Name=TNFSF8 {ECO:0000313|RefSeq:XP_014931799.1}; OS Acinonyx jubatus (Cheetah). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Laurasiatheria;…

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UniProtKB – Q27974

UniProtKB – Q27974 <p>An evidence describes the source of an annotation, e.g. an experiment that has been published in the scientific literature, an orthologous protein, a record from another database, etc.</p> <p><a href=”www.uniprot.org/manual/evidences”>More…</a></p>&#13; Skip Header You are using a version of browser that may not display all the features…

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java – Calculating physico-chemical properties of amino acids in Biojava

I need to calculate the number and percentages of polar/non-polar, aliphatic/aromatic/heterocyclic amino acids in this protein sequence that I got from UNIPROT, using BioJava. I have found in the BioJava tutorial how to read the Fasta files and implemented this code. But I have no ideas how to solve this…

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How to create a subset FASTA file of proteins of interest based on UniprotKB AC / Accession Numbers –

Hello, I am looking to create a subset FASTA file from an existing FASTA file. The subset file should only include entries with certain accession numbers. I have created a BioIndexed File with the correct number of entries, but I am unsure how to use the getsubset function in this…

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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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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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UniProt: A0A1S3QEZ7_SALSA

ID A0A1S3QEZ7_SALSA Unreviewed; 104 AA. AC A0A1S3QEZ7; DT 12-APR-2017, integrated into UniProtKB/TrEMBL. DT 12-APR-2017, sequence version 1. DT 02-JUN-2021, entry version 11. DE SubName: Full=lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog isoform X2 {ECO:0000313|RefSeq:XP_014038412.1}; GN Name=LOC106591717 {ECO:0000313|RefSeq:XP_014038412.1}; OS Salmo salar (Atlantic salmon). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Actinopterygii;…

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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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Proteomics | EMBL-EBI Training

Feedback and help Who is this course for? An undergraduate degree in a life science subject or some background knowledge on the composition of proteins, would be an advantage. What will I achieve? By the end of the course you will be able to: Describe what is meant by…

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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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Index of /refseq

Name Last modified Size Parent Directory – B_taurus/ 2020-02-25 11:45 – D_rerio/ 2020-02-25 11:46 – FunctionalElements/ 2020-08-13 18:17 – H_sapiens/ 2020-02-25 11:39 – LocusLink/ 2007-04-27 08:08 – MANE/ 2021-06-16 13:56 – M_musculus/ 2020-07-17 15:40 – R_norvegicus/ 2020-02-25 11:44 – S_scrofa/ 2020-02-25 11:44 – TargetedLoci/ 2016-08-09 11:27 – X_tropicalis/ 2020-02-25 11:45…

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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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Is there any tutorial to access Gene Ontology (GO) terms in R?

Is there any tutorial to access Gene Ontology (GO) terms in R? 0 Hi, I was wondering if we can access GO terms in R using QuickGO or other tools. I have a huge list of UniprotKB for which I need to create a data set of GO terms and…

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Is the Ensembl GRCh38 genome assembly more up to date than the UniProtKB online database?

Dear all, I am working with a list of Ensembl accession codes for a desired group of proteins. I have downloaded the protein annotations related to the genome assembly GRCH38. I fetched the genomic coordinates from UniProtKB API service using the Ensembl accession codes. The service provide a protein annotation…

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Accessing Uniprot Info Via Python

Accessing Uniprot Info Via Python 2 Does anyone here regularly access uniprot info using python? If so how? I tried downloading github.com/boscoh/uniprot through github but was unable to figure out the installation. What does everyone here use? python uniprot • 8.7k views • link updated 3 hours ago by Nick…

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