Hi all,
I work with the antibody sequences (length = ~400-450 bp) and have the data from 454 platform.
From this data I want to find the sequences that are clonally related to the template or reference antibody sequence that I have. Clonally related sequences share the highly homologues CDR3 motif which is ~40-50bp long sequence present in the antibody sequence.
Schematic of antibody seq:
|-----------------------------------**********-----------------------|
***** is the CDR3 motif.
Question- I want to find the sequences from 454 data that has the same or highly homologous motif of interest in it. Which tools, programs would be useful for me. Any help/directions would be very helpful. ps- I'm beginner in bioinformatics field.
Thank you.
Try emboss utilities if you know the sequence:
fuzznuc.sh: search for patterns in nucleotide sequences
fuzztran.sh: search for patterns in protein sequences (translated)
Best Wishes,
Umer
Thanks Umer! Yes I know the sequence (I mean I have a known antibody sequence with CDR3 motif), I've never used emboss but will try. And how about BLASTing 454 reads against the 40-50 bp long CDR3 motif of this known antibody sequence, do you think its a good idea or I'll miss the hits from 454 data?
Thanks very much!
Yeah you may do that, but use a local alignment tool by making your original 454 data as a database and your motifs as a query sequence and using something like SWIPE
Yes sure, you may contact me if you get stuck!
Best Wishes,
Umer
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