How to show whole blast contig

Question

[Paul]

Dear all,

I created Embedding Blast Tool In A Website and after blasting I can see (which is typically output) just part of my contig. Do you have any idea how to show up whole contig?

Thank you so much for any help,

Paul.

[h.mon]

What do you mean by "see just part of my contig"? You want to see all your query sequence, or all the subject sequence?

What happens is BLAST trims the output to show only regions above specified thresholds, so poor similarity is left out. You may tweak the parameters to increase the region BLAST considers as "good similarity", but even then, very low similarity regions will be left out of the output.

[Paul]

Hello, thank you for reply. Yeas I was thinking all the subject sequence, because when i BLAST my query toward my reference sequence, i can see just matching position, but I would like to extract whole part of reference contig of my FASTA file.. I hope right now it is clear.

Answer 1

[h.mon]

(Based on your C: How to show whole blast contig):

You can use blastdbcmd (BLAST+) or fastacmd (old BLAST) to retrieve the whole subject sequence. Read the excellent blog from Peter Cock to learn some blastdbcmd oddities (for example here and here).

[deepti1rao]

Can BLAT be used for the same purpose?? I need the entire contig to be showing up at a stretch