how to find sequence in ref

[thisisnotsound]

Hi

I am quite new in genomics and bioinformatics. I am a vet trying to do some research on pathogenic bacteria.

I have a simple and maybe stupid question.

I have the reference genome of a bacteria, and I want to find location of sequences (e.g. PCR primer sequences or any gene sequences).
I tried IGV and some DNAStar tools, but or I don't get results (i think due to mismatch), or an alignment is made and the "non overlapping" sequences are removed so I can't "see" where it is in the ref genome nor the connection with annotations.

Is there a tool to just simply open a ref and then input a sequence what "finds" it's place?

thanks

Zoli

[yzzhang]

you can give the software abacashttp://abacas.sourceforge.net/ a try

[GenoMax]

How long is the sequence you are trying to find a match for? Do you need a visual (GUI) program or can you use unix command line?

[thisisnotsound]

100-1000 bp pcr products usually.

GUI would be nice, I cant't read the matrix (yet)...

[GenoMax]

You could try blast2sequences at NCBI: http://blast.ncbi.nlm.nih.gov/Blast...._LOC=align2seq

It may be easy to use blat for this type of analysis though there isn't a location I know of that can accept the 2 sequences via a GUI.

[thisisnotsound]

Yes, I see those ways, I am already working with a bioinformatic expert, he does the scripting for my questions
I was just wondering about a simple (=running on windows, graphic interface, dummy-friendly) program to work with when I am alone

I just would like to load a genome, input some sequence and observe where and how it aligns

[GenoMax]

Don't think there is a free local GUI alignment program for windows. There are commercial ones (CLC, Geneious etc).

Ask your bioinformatics person to show you how to use linux in a virtual machine. If your needs are limited to this one application then you should be able to use blat in linux virtual machine.

If the programmer can write a GUI interface on windows then perhaps (s)he can use the mappacbio8k.sh from BBTools (which is a java program and can run natively on windows).

[thisisnotsound]

Thanks, I can make a virtual machine and also not hopeless in using consoles and writing scripts, if it is necessary I will. I was just asking if there is an easier way.

[GenoMax]

If you are comfortable with VM's then go the blat route. Results will be fast (with a bacterial genome) and you won't have to do any scripting (unless you want to parse the blat result in some way).

[thisisnotsound]

ok, thanks.