How Do I Align More Than Five Long Dna Scaffolds (Contigs) To The Reference Gene?

Question

[biostar]

Hi everyone, I tried to align one of my reference genes with its contigs using Mauve, MAFFT, emboss needle etc, but could not get it aligned locally (I also needed to show the aligned sequences) . Is there any program I can use to do the local pairwise alignment of multiple sequences?? I just need to map the contigs to my reference gene and find the UTR regions and introns. Any inputs would be appreciated on this.. Thanks!!

[Pavel Senin]

you may want to try MUMmer - plotting your gene(s) on Y and contigs on X. the tool would plot diagonal bands (where the common elements are) which can shed some light on how things are arranged and assembled.

[biostar]

Thanks Pavel! I already tried this, but I also need to show the alignment of all sequences locally. I might need to do it manually using SeAl..

[User000]

hi,

Which command line did you use to generate a plot like this? Thanks

Answer 1

[Zev.Kronenberg]

I would suggest lastz:

http://www.bx.psu.edu/~rsharris/lastz/

I have used it to align whole chromosomes between divergent species. It has a flexible output and is efficient.

[biostar]

Thank you Zev, but this program somehow generates error on installation..

[biostar]

Found this tool on NCBI, where I can input reference sequence and target sequences (Multiple) and gives nice result of pairwise alignment (local): http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=align2seq

Answer 2

[Darked89]

Late but hopefully not too late. One can map anything from genome to genome (and obviously genes to contigs) up to FASTQ short reads using LAST: http://last.cbrc.jp/

LAST has tools to convert the output from MAF to SAM, so results are viewable in IGV. And using another path, it can output dotplots as well (see the web page).