comparison of several genomic regions with BLAST

Model Organism: Worms WormBase
1

I’d like to know how to compare several genomic regions (i.e. 18S of a group of nematodes) … in order to see which sequences are common.

2

one idea would be to use the C.elegans sequences as seeds and try to pull homolg sequences from GenBank/DDBJ/ENA … but you might want to realign the sequences, as blast can be a bit crude, but ymmv

3

Hi
You can align the sequences using this Programme called “Clustal W” at http://www.ebi.ac.uk/Tools/clustalw2/index.html

From this you can get the common region/sequence of similarity

Hope this helps… :slight_smile:

Luv

4

have a look at

The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies
, Patrick Schloss PLoS Comput Biol, Vol. 6, No. 7. (8 July 2010), e1000844.

http://dx.doi.org/doi:10.1371/journal.pcbi.1000844

for some pitfalls