Question: Remove Motif Sequence From The Fasta File Of Sequences
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gravatar for tarakaramji
3.5 years ago by
tarakaramji10
tarakaramji10 wrote:

Dear colleagues! I have a file with sequences in FASTA format. I want to remove part of sequence with known coordinates from the fasta file. In detail, i have a file1 with sequence ID with coordinates and file 2 has the fasta sequences of all that were mentioned in the file1. taking this coordinates into consideration from file1, matching them with fasta file2 and get the sequence without the mentioned coordinate part sequence. Any help would be highly appreciated.

fasta perl bioperl • 1.3k views
ADD COMMENTlink modified 3.5 years ago by swbarnes22.8k • written 3.5 years ago by tarakaramji10
1

Could you please write an example of what you need to get done? It's hard to understand from verbal description only.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Biomonika (Noolean)3.0k

This falls into the category "parse a FASTA file and do something with it." As you have tagged your question "perl/bioperl", step 1 is "learn how to parse a FASTA file using those tools". So start with the SeqIO how-to.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Neilfws47k
0
gravatar for swbarnes2
3.5 years ago by
swbarnes22.8k
United States
swbarnes22.8k wrote:

Rather than make a perl solution, you could try BEDTools. It should be able to get you the intersection of a fasta file with a .bed file of coordinates.

ADD COMMENTlink written 3.5 years ago by swbarnes22.8k
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