Question: Convert BLAST format to EMBL file format
0
gravatar for User000
2.9 years ago by
User000260
User000260 wrote:

Hello,

I would like to change a BLAST formatted file (XML, tab etc.) to EMBL format. I don't think there is a direct converter, but may be some of you knows how to do it and if there are ways to do it. Any tips are appreciated. Thanks in advance

blast embl • 1.1k views
ADD COMMENTlink modified 2.9 years ago by ivivek_ngs4.7k • written 2.9 years ago by User000260

I don't think there's a direct converter either, because those are completely different formats for different purposes. BLAST contains sequence local alignment information. EMBL contains a rich description of a single sequence or set of sequences.

Perhaps what you want to do is retrieve the sequences of the BLAST hits in EMBL format?

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Neilfws48k

I am not very much interested in having the alignment sequence itself, but the information, like where so the seq-s start to align, e-value and put all of these in EMBL format..so that when I use i.e. Genome View, I can see where and how my contigs map on that genome..I don't if I should use bam format then? But, I have only few short contigs..

ADD REPLYlink written 2.9 years ago by User000260
0
gravatar for ivivek_ngs
2.9 years ago by
ivivek_ngs4.7k
Seattle,WA, USA
ivivek_ngs4.7k wrote:

ReadSeq should be able to serve the purpose for you. Take a look at this link. Should be able to serve the purpose you are trying to achieve.

ADD COMMENTlink written 2.9 years ago by ivivek_ngs4.7k
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