Alignment DNA sequence tool

Question

[jaqy]

Hello,

Please can you give me a tool which return the score of alignment of all the 8-mer motifs between a DNA sequence (own sequence) and a set of sequences (22 500 sequences)?

Thank you

[Brian Bushnell]

Can you further explain exactly what you wish to accomplish?

[jaqy]

Hello

thank you Brian Bushnell for your reply

I have a sequence of 1000 pb and I would like detect all the octamer pattern in this sequence and give a score for each detected pattern

Answer 1

[Yongjie Zhang]

You may perform blast2 on the NCBI website with your own sequence as query and the 22500 sequences as subject although I'm not sure what's the max. number of subject sequences allowed. If that does not work, you may try local blast with the tabular output.