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How to search the short sequence among the nuclear acid bank

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

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How to search the short sequence among the nuclear acid bank

Postby 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!
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Postby 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.

Cis or trans? That's what matters.
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