How To Do Multi-Sequence Alignment Of Scaffolds ?

Question

[MAPK]

Hi everyone, I need to align scaffolds, CDS and transcripts (local alignments) and see the aligned/nonaligned and the coding and noncoding regions. I have a fasta file with one transcript, CDS and multiple scaffolds and I need to allign all of those. Could you please suggest me any program that I can use? I heard bowtie can be used in this case?? Thanks a bunch!

[Josh Herr]

Are you trying to align short read data (RNA-Seq, etc.) to a reference sequence? What exactly are you trying to do? It sounds like you are confused about what you are doing.

[Devon Ryan]

Are you trying to get a multisequence alignment? Is there a reason you mentioned bowtie? It's not normally used to align contigs (that's not really its forte).

[MAPK]

@dpryan79, Thanks for replying to my thread. Yes I am trying to do multisequence alignment and I just mentioned Bowtie because someone told me to try Bowtie. Is there any program you know I could use in this case?

Answer 1

[Adrian Pelin]

Hello,

I suppose you have your reasons for aligning CDS features to scaffolds.

I would suggest bwa. I am currently working with it, and find the results acceptable.

There is a short intro by a Broad member arguing BWA being the balance between performance and accuracy. https://www.broadinstitute.org/files/shared/mpg/nextgen2010/nextgen_li.pdf

I suggest indexing your scaffolds, and aligning CDS features to scaffolds as opposed to the other way around.

Adrian

Answer 2

[Devon Ryan]

For multisequence alignment, just have a look at this page for a number of options.

[MAPK]

But how do you do local alignment of multiple sequence? I cannot use global alignment for these sequences.

[Devon Ryan]

I don't think I've ever seen multiple sequence alignment programs use global alignment, it wouldn't make much sense. I'm assuming that you know what multiple sequence alignment actually is and how it differs from what bowtie/bwa/etc. do, though perhaps that's an incorrect assumption.