Tag: SwissProt

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…

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  …

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…

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…

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,…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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….

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…

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…

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…