User: pwg46

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pwg46360
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United States
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3 years, 11 months ago
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4 years, 9 months ago
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Posts by pwg46

<prev • 23 results • page 1 of 3 • next >
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Aligning UniProt Canonical Sequences With Their Isoform Sequences
... Hello, I notice that when I input a UniProt into UniProt's website, the result page has an "Alternative Sequence" section, which shows exactly how and where each of the UniProt's isoforms differ from the canonical sequence. I am unable to find this information in any of UniProt's ftp files. Could s ...
sequence canonical align isoform uniprot written 4.0 years ago by pwg46360 • updated 4.0 years ago by Elisabeth Gasteiger1.6k
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How to tell if a RefSeq or UniProt protein identifier is human?
... Hello, I am creating a local table to convert from RefSeq protein identifiers (E.g,NP) to UniProt identifiers. RefSeq has a file named "gene_refseq_uniprotkb_collab.gz" on their FTP server, which contains mappings from RefSeq protein to UniProt. However, there are 18 million mappings, and I want to ...
refseq protein uniprot human written 4.0 years ago by pwg46360 • updated 4.0 years ago by Elisabeth Gasteiger1.6k
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Protein Sequence Alignment
... Say I am given a protein U1 from the Uniprot database. And, according to UniProt's mapping data file, U1 maps to R1 in RefSeq's protein database. While U1's and R1's sequences are very similar, len(R1)>len(U1), I am guessing because R1 contains some extra region. What is an efficient way to align ...
refseq sequence protein uniprot alignment written 4.2 years ago by pwg46360 • updated 4.2 years ago by dago2.5k
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RefSeq Version Numbers/Mapping File
... Hello, I notice that the refSeq db's data files contain refSeq transcripts, proteins, etc. with version numbers. I am wondering approximately how often these version numbers change? Also, is it likely that two Refseq transcripts, which are the same transcript (but different versions), would have di ...
refseq version protein mapping transcript written 4.2 years ago by pwg46360 • updated 3.5 years ago by Biostar ♦♦ 20
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Data File Which Maps Between Gene Names and Uniprot Protein ID's
... Hello, I am looking for a data file, which provides mappings between Gene Names and Uniprot Protein ID's. For example, entering ERN2 refers to Q76MJ5 when entered into Uniprot's website. Thanks   ...
gene name data uniprot file mapping written 4.2 years ago by pwg46360 • updated 4.2 years ago by Elisabeth Gasteiger1.6k
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Ensembl Gene Sequence Data File?
... Hello, I am looking for a sequence file for Ensembl gene identifiers. In particular, I have been searching for a file like the CDS (Fasta) file here http://www.ensembl.org/info/data/ftp/index.html, which simply maps ENSTs to their coding sequences. So, I'm wondering if there is a file like that for ...
ensg fasta sequence data ensembl written 4.3 years ago by pwg46360 • updated 4.3 years ago by Tariq Daouda210
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Comment: C: Does RefSeq DB have a CDS file for its transcripts?
... Hmm, I looked into that. However the data file it outputs doesn't give the actual sequences. Are there any adjustments I could make to get the actual sequence? ...
written 4.4 years ago by pwg46360
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Does RefSeq DB have a CDS file for its transcripts?
... Hello, I am looking for a file which contains all CDS for their NM (coding transcript) identifiers. Ensembl has one which maps each of its ENST's to their CDS, however I have been unable to find the same for Refseq's coding transcripts (NM). If anyone knows of and could point me to such a file, tha ...
nm sequence coding refseq cds written 4.4 years ago by pwg46360 • updated 4.4 years ago by Irsan6.8k
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How does RefSeq get their transcript sequences?
... I have been looking at the rna.fa.gz file in RefSeq's database. For the majority of the NM's, the sequences don't start with ATG. So, I thought perhaps the rna file was containing the entire sequence of the mRNA and not just the coding slices. So, I took an NM, the chromosomal CDS start position and ...
atg nm sequence refseq identifier written 4.4 years ago by pwg46360
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Comment: C: How does RefSeq Calculate their Positions?
... Hmm, interesting. But NM's are not always perfect matches with an ENST that maps to it? I'm basically just trying to figure out how to connect RefSeq transcript to my node graph of other identifiers (ENST,ENSG,ENSP,grch38 chromosome,uniprot, refseq protein). But in order to connect Refseq transcript ...
written 4.4 years ago by pwg46360

Latest awards to pwg46

Appreciated 4.2 years ago, created a post with more than 5 votes. For GRCh37/38(NCBI) vs hg19/hg38(UCSC)
Popular Question 4.4 years ago, created a question with more than 1,000 views. For GRCh37/38(NCBI) vs hg19/hg38(UCSC)
Student 4.4 years ago, asked a question with at least 3 up-votes. For GRCh37/38(NCBI) vs hg19/hg38(UCSC)

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