Genomic Alignment Of Intergenic Region

Question

[Pcrer]

Hey, guys.

Again, I wanna make an alignment of intergenic region, I cannot find better solutions? Anyone can help me?

Many thanks.

[Chris Miller]

Please be more specific about what you're trying to do. What kind of input data do you have, what are you trying to do with it, and what should your output be? As is, it's nearly impossible to answer your question.

[Larry_Parnell]

Also, your question implies that you tried some tools or processes. Please tell us what those were and why you feel they were unsatisfactory.

[Michael]

Another question bot?

[Pcrer]

Thanks for all. just holidays for a while. I just want to make an alignment which is far away (200K) from my target gene, what I have is the sequence data from online sequence database, nothing else.

Answer 1

[Rm]

MUMmer - MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. You can try aligning intergenic regions and share your experience.

you can search some more alignment programms here

[Pcrer]

thanks a lot, I am try to learn it.

Answer 2

[Casey Bergman]

Pollard et al. have conducted simulation analyses of pairwise and multiple aligners for noncoding DNA in species like Drosophila that may help guide your choice of aligner:

http://www.ncbi.nlm.nih.gov/pubmed/16904011

http://www.ncbi.nlm.nih.gov/pubmed/14736341

[Pcrer]

Huge bioinformatics work will be a problem for me.