[BiO BB] Search a Profile against a sequence database

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Thu Sep 9 10:43:31 EDT 2004

On Thu, 9 Sep 2004, Raj wrote:

>       I need a gapless alignment. PSIBLAST does not have a gapless
>alignment option. Thanks for the answer though.

Do you mean global alignment?

SAM and HMMER both have a 'global global' option (I think) for HMM to
sequence alignment. You can find tools to convert a psiblast profile into
a HMM. Don't have the details right now though.

>On Wed, 8 Sep 2004 17:27:43 -0400, Ryan Golhar <ryangolhar at hotmail.com> wrote:
>> You can use PSI-BLAST.  Generate your sequence database using formatdb
>> from the NCBI toolkit, and then use PSI-BLAST to search your custom
>> database using your profile...
>> -----
>> Ryan Golhar
>> Computational Biologist
>> The Informatics Institute at
>> The University of Medicine & Dentistry of NJ
>> Phone: 973-972-5034
>> Fax: 973-972-7412
>> Email: golharam at umdnj.edu
>> Hi all,
>>      I am looking for some tool that enables me to search a (custom)
>> sequence database using the 'profile' (BLAST generated) of the query
>> sequence rather than a query sequence itself. If anyone is aware of any
>> such tool, please let me know.
>> Regards,
>> Raj
>BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org

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