How to search the short sequence among the nuclear acid bank

Everything on bioinformatics, the science of information technology as applied to biological research.

Moderators: honeev, Leonid, amiradm, BioTeam

Post Reply
seahow
Garter
Garter
Posts: 6
Joined: Wed Mar 31, 2010 7:04 am

How to search the short sequence among the nuclear acid bank

Post by seahow » Sat Oct 22, 2011 2:30 am

Hi,I want search some consensus in the genome using blast program on human genome database. But when I enter the sequence which is about 10 base long , the BLAST show me “No significant similarity found” I have enlarge the expect threshold to 10000. And the sequence I entered is really in the human genome.

Should I change the program but blast? Or others, thanks!

User avatar
JackBean
Inland Taipan
Inland Taipan
Posts: 5694
Joined: Mon Sep 14, 2009 7:12 pm

Post by JackBean » Sat Oct 22, 2011 8:48 am

try the NCBI BLAST, it should automatically set for short sequences. There are also some algoritms for searching consensus sequences, whit AAs far from each other.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

Post Reply

Who is online

Users browsing this forum: No registered users and 0 guests