Question: How Do I Align More Than Five Long Dna Scaffolds (Contigs) To The Reference Gene?
7
gravatar for biostar
6.4 years ago by
biostar150
biostar150 wrote:

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!!

pairwise alignment reference • 5.5k views
ADD COMMENTlink modified 4.8 years ago by Darked894.2k • written 6.4 years ago by biostar150
2

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.

enter image description here

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by Pavel Senin1.9k

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..

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by biostar150

hi,

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

ADD REPLYlink written 4.8 years ago by User000380
3
gravatar for Zev.Kronenberg
6.4 years ago by
United States
Zev.Kronenberg11k wrote:

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.

ADD COMMENTlink written 6.4 years ago by Zev.Kronenberg11k

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

ADD REPLYlink written 6.4 years ago by biostar150
1

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

ADD REPLYlink written 6.4 years ago by biostar150
3
gravatar for Darked89
4.8 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

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).

ADD COMMENTlink written 4.8 years ago by Darked894.2k
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