Tag: SwissProt
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…
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,…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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….
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…
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…
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…