Search of sequences of interest in the 454 data

Question

[GP]

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.

Answer 1

[umer.zeeshan.ijaz]

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

[GP]

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!

[umer.zeeshan.ijaz]

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

[GP]

Great, thanks again! I will try the 2nd option-searching motif against 454 database. Is it possible to contact you again I just in case if I have more questions.

Best Regards, G

[umer.zeeshan.ijaz]

Yes sure, you may contact me if you get stuck!

Best Wishes,

Umer