How To Blast Multiple Contigs To The Reference Database?

Question

[vibhanim.21]

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 ...

Answer 1

[Sandeep]

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

[vibhanim.21]

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

Answer 2

[ipb727258]

for plasmid search, use online CGE server https://cge.cbs.dtu.dk/services/PlasmidFinder/