Question: How To Blast Multiple Contigs To The Reference Database?
1
gravatar for vibhanim.21
6.2 years ago by
vibhanim.2140
Manipal University
vibhanim.2140 wrote:

i have multiple contigs in fasta format after assembling the reads. i also have 33 reference genome sequences. i want to blast the query sample sequence to my reference sequences as well as the plasmID database to find the plasmid regions. but is there any other way i can find similarity between the sequences ? because am unable to do the NCBI mega blast for those... please do help me ...

assembly next-gen blast alignment • 4.2k views
ADD COMMENTlink modified 6.2 years ago by Sandeep250 • written 6.2 years ago by vibhanim.2140
2
gravatar for Sandeep
6.2 years ago by
Sandeep250
Manipal, India
Sandeep250 wrote:

You could try to download and install blast locally. You can create a custom blastDB (of all 33 reference genome and plasmID) and blast your fasta sequences against it. The procedure has been documented extensively on NCBI.

Also, there are options online to do custom blast. You could check out http://bioapp.psych.uic.edu/Overview.htm were they have options to blast multiple fasta against custom refence fasta and also multiple fasta against NCBI database. Hope this helps

ADD COMMENTlink written 6.2 years ago by Sandeep250

thank you i tried the above...and got the results..

ADD REPLYlink written 6.2 years ago by vibhanim.2140
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