User: Tom

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Tom30
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Last seen:
7 months ago
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4 years, 3 months ago
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Posts by Tom

<prev • 66 results • page 1 of 7 • next >
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Comment: C: Download all peptide sequences from NCBI in fasta format?
... Just to your earlier point about the number of sequences, is it possible to add a filter to only pull down in fasta sequence below a max length? Because i can see what you're saying, some just say peptide in the header but are full proteins, i just want to make a test set so pulling out the shorter ...
written 7 months ago by Tom30
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Comment: C: Download all peptide sequences from NCBI in fasta format?
... this is fantastic thank you ...
written 7 months ago by Tom30
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Download all peptide sequences from NCBI in fasta format?
... I want to download in fasta format all the peptide sequences in the NCBI protein database (i.e. > and the peptide name, followed by the peptide sequence), I saw there is a MESH term describing what a peptide is here, but I can't work out how to incorporate it. I wrote this: import Bio f ...
biopython written 7 months ago by Tom30 • updated 5 months ago by Biostar ♦♦ 20
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How to run PSSPred on multple sequences
... Hi all, I'm using PSSpred [link here][1] to predict secondary structures for a set of peptides. I am running the command on linux. When I run the command on a fasta file with a single sequence in it like this: perl PSSpred.pl test.fasta it works (i.e, it correctly predicts the secondary stru ...
psspred sequence peptide written 2.2 years ago by Tom30 • updated 2.2 years ago by Pierre Lindenbaum129k
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... I know, it seems like this would be relatively straightforward, it's very frustrating. Unfortunately, I am not an expert in this particular area, so I don't feel like I know enough (yet) to try and find a workaround or understand exactly what's happening. ...
written 3.1 years ago by Tom30
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... Thank you; I emailed back the help desk to ask them why the file was being truncated (this happened whether I was at home or in work); they replied: Unfortunately, web displayed citation format is NOT a format supported by API. There is no good way to regenerate that format through fetched content ...
written 3.2 years ago by Tom30
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... Yes no problem, so this is my xtract.Darwin: http://www.filehosting.org/file/details/664811/xtract.Darwin and this is my tmp.xml (for GDS4925, the dataset in above example): http://www.filehosting.org/file/details/664812/tmp.xml Thanks for your help. I've also emailed back the help desk to ask t ...
written 3.2 years ago by Tom30
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... I appreciate it; Everything works great, until step 4, where I get no output at all, so there is no error I can paste (and I checked, tmp.xml is not empty). I emailed the NCBI help desk this question: > I have a list of GEO data set accession (e.g. GDS4925) and I want a > reference for each ...
written 3.2 years ago by Tom30
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... Thanks so much, I officially give up I think I'd rather do >100 references manually at this stage. Command 1 works (as in gives me the tmp.xml file); command 2 doesn't work (no output). So I re-installed e-utils: localhost:~ Aoife$ cd ~ localhost:~ Aoife$ perl -MNet::FTP -e \ '$ftp = ne ...
written 3.2 years ago by Tom30
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Comment: C: Extract Bibliographic Reference from GEO dataset using EFetch?
... I really appreciate it. I think there's something wrong with either my computer (just a standard mac terminal) or my connection to entrez. As you can see from the attached image [here][1], even when I type the first command, I just don't get the PMID back. Thank you for your help though, I appreciat ...
written 3.2 years ago by Tom30

Latest awards to Tom

Supporter 7 months ago, voted at least 25 times.
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Popular Question 2.6 years ago, created a question with more than 1,000 views. For Convert read counts to RPKM or TPM values: Numbers don't look right?

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