User: massa.kassa.sc3na

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Posts by massa.kassa.sc3na

<prev • 11 results • page 1 of 2 • next >
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Answer: C: BLAST using Biopython
... few problems: You pass the STRING "filename" to the NCBIWWW.qblast call instead of variable. If the file from `input` should be FASTA file, then you need to pass `file_name` variable (without quotes) and the `open(..).read()` is not necessary. ...
written 1 day ago by massa.kassa.sc3na30
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Comment: C: extract genes and functions +/-50kb around a SNP
... Hi, well if you only want genes, then I would suggest downloading complete gff or similar format for your organism, and then do simple selection of rows within desired range. In good gff, there is already some functional annotation present, but with accession number for the gene you certainly will b ...
written 3 days ago by massa.kassa.sc3na30
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Answer: A: How do I extract locus-position information from XMFA file? Start-end positions
... Hi, I assume that you are talking about file like this: http://darlinglab.org/mauve/user-guide/files.html (I took the example as a SAMPLE_FILE) >seq_num:start1-end1 ± comments (sequence name, etc.) Do you need to extract the seq_num and the start1, end1 indices? This can be done with **gr ...
written 8 days ago by massa.kassa.sc3na30
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Comment: C: tcoffee psicoffee mode local blast error
... Hi, I assume that you are trying to run psicoffee. The most simplest solution from my point of view is to used -mode psicoffee without any -blast_server parameter. This will (according to the docs [here][1]) default to using web-service at EBI and you dont need to worry about anything. If you rea ...
written 10 days ago by massa.kassa.sc3na30
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Comment: C: tcoffee psicoffee mode local blast error
... How did you "gave path" to legacy_blast.pl? I would suggest to: 1) check if legacy_blast.pl is in your PATH (in terminal run "which legacy_blast.pl"), response should be a path to that file, if not then continue with 2. If it is in your path, then it may not be visible for t-coffee (maybe the tool ...
written 11 days ago by massa.kassa.sc3na30
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Comment: A: Filter unique values from col1 and print the dataset using unix_large dataset
... To filter out rows based on value in Col1 do `awk '!x[$1]++' < YOURFILE` the `$1` being the first column (not the column name). Beware that `$0` checks if whole row is unique. So if you want to filter based on second column you would write `awk '!x[$2]++' < YOURFILE`. See `man awk` for more i ...
written 12 weeks ago by massa.kassa.sc3na30
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Reinfrorce motif search with knowledge of protein sequence / structure
... Hi everyone, I'm doing some work with DNA motif discovery - especially with TF binding sites (usually sigma factors which have dual motif (-10 and -35 site)). In our case the sigma factors have known protein sequence, with known conserved domains etc. I was wondering if there is some way - or som ...
motif protein written 3 months ago by massa.kassa.sc3na30 • updated 3 months ago by ATpoint17k
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Answer: A: How to pass multiple seq_start and seq_stop statements to NCBI efetch
... Hi, so it might be help to anyone in future: after consulting with NCBI Entrez support, it appears that this functionality isn't and will not be supported. It's a shame. So don't waste your time and for-loop forever. Good guys wrote: *No that will not be possible. The starts and stops must be singl ...
written 2.7 years ago by massa.kassa.sc3na30
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Comment: C: How to pass multiple seq_start and seq_stop statements to NCBI efetch
... Hi, Than you for reply. I know that I can do that in a for loop, (and currently doing so); But since I want to fetch relatively short fragments, I want to fetch them all witch one command (reasonable number) to limit the calls to NCBI server. Or am I missing something and this is what the UNIX e-ut ...
written 2.8 years ago by massa.kassa.sc3na30
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How to pass multiple seq_start and seq_stop statements to NCBI efetch
... Hi, I wasn't able to find anywhere how to pass several seq_start and seq_stop optional arguments to list of queries for NCBI efetch. See this: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=433294648rettype=fasta&seq_start=100&seq_stop=200 server ansver: > ...
ncbi efetch sequence entrez written 2.8 years ago by massa.kassa.sc3na30

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