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!!
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).