Question: Search of sequences of interest in the 454 data
0
gravatar for GP
5.6 years ago by
GP10
Sweden
GP10 wrote:

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.

454 antibody sequence • 1.4k views
ADD COMMENTlink modified 5.6 years ago by umer.zeeshan.ijaz1.7k • written 5.6 years ago by GP10
1
gravatar for umer.zeeshan.ijaz
5.6 years ago by
Glasgow, UK
umer.zeeshan.ijaz1.7k wrote:

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

ADD COMMENTlink written 5.6 years ago by umer.zeeshan.ijaz1.7k

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!

ADD REPLYlink written 5.6 years ago by GP10

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

ADD REPLYlink written 5.6 years ago by umer.zeeshan.ijaz1.7k

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

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by GP10

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

Best Wishes,

Umer

ADD REPLYlink written 5.6 years ago by umer.zeeshan.ijaz1.7k
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