program to match sequences - (Jan/29/2014 )

Hallo all,

I am looking for a program that I can use to check whether certain sequences are present in my plamids.

The problem is: when 1 amino acid is different than I can not find the sequence in my plasmid.

I want a program that, for example, would still "match" the sequences while mentioning that 1 base is different.

for example, the sequence of my plasmid is:

... TGTGTCCCTAAATCGT....

and the "gene" is: TGTGTCCGT, than I would not find it because I have that G rather than a C.

Any ideas or suggestions?

I just want to check for certain genes even if there is a small difference.

-lyok-

perhaps with BLAST and the megablast option?

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

-hobglobin-

You can use clustalw. If you are a windows user it is included in BioEdit which is free. There afe also many other options, you're basically looking for a sequence alignment program.

-mboss-

mboss on Wed Jan 29 20:39:08 2014 said:

You can use clustalw. If you are a windows user it is included in BioEdit which is free. There afe also many other options, you're basically looking for a sequence alignment program.

Ok, I'll check that one.

hobglobin on Wed Jan 29 20:31:49 2014 said:

perhaps with BLAST and the megablast option?

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

No, because I want to compare my sequence with sequences from certain genes.

Or is there a way I can do this using NCBI?

I have 1 sequence (the plasmid) and I want to find certain genes in this plasmid (like for example a drug resistance gene).

I want to match those genes woth the plasmid (see if the gene is really in the plasmid or not)

-lyok-