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Forum: Shell Programming and Scripting 09-25-2014

Parsing and masking regions from a single fasta file with subsequence

1,334

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The content in the file >CP008559...

The content in the file

>CP008559 Pseudomonas aeruginosa SRS4, complete genome
tttaaagagaccggcgattctagtgaaatcgaacgggcaggtcaatttccaaccagcgat...

Forum: Shell Programming and Scripting 09-25-2014

Parsing and masking regions from a single fasta file with subsequence

1,334

Posted By

Parsing and masking regions from a single fasta file with subsequence

HI,

I have a Complete genome fasta file and I have list of sub sequence regions
in the format as :
4353..5633
6795..9354
1034..14456

I want a script which can mask these region in a single...

Forum: Shell Programming and Scripting 12-30-2013

Shell script for changing the accession number of DNA sequences in a FASTA file

2,681

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---------- Post updated at 08:44 AM ----------...

---------- Post updated at 08:44 AM ---------- Previous update was at 08:44 AM ----------

it worked nicely. Thank you

Forum: Shell Programming and Scripting 12-30-2013

Shell script for changing the accession number of DNA sequences in a FASTA file

2,681

Posted By

Shell script for changing the accession number of DNA sequences in a FASTA file

Hi,

I am having a file of dna sequences in fasta format which look like this:
>admin_1_45
atatagcaga
>admin_1_46
atatagcagaatatatat

with many such thousands of sequences in a single file. I...

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