Gene Sequencing Alignment Problem

anonya

New member
Nov 16, 2015
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#1
Greetings,



I'm trying to align an 800-amino-acid sequence coded by a gene from a

known genome to a large set of ordered contig sequences from a new

genome of a related strain whose sequence is not yet fully resolved.



Using tblastn, I've so far been unsuccessful in finding

positions/sequence sections that align well to the sequence

from the gene of interest and also do not align better to another

sequence from another gene.



Effectively, sequences that have the best alignment to a gene get

'taken' by that gene, leaving the gene of interest with no significant

alignments. Thus, I’m unable to map the position/sequence sections of

this gene among the contigs.



Is there a way I can decisively check whether or not this gene exists

in its entirety, or partially, in the contig set

of the newly sequenced genome, and if yes, determine its location?



Or is there something inherently flawed about my method/approach that

I could please get a recommendation as to how to correct?
 

yia7

New member
Mar 2, 2017
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#2

Perhaps, try the nucleitide level first. also, make sure sequence is going in the correct direction. If you know the ORF sequence, you could search for that within your new sequence to make sure you are on the right track to start. Does this answer your question?