Post by Thomas JahnsPost by JoeTi'm trying to do a genome (i think) comparison between A. agrarius, R
novegius, C glareolus and being new to bioinformatics, i'm not exactly
sure what would be the best nucleotide or genome part that i should
select is doing a multiple sequence analysis.
can someone point me to the correct thing i should do?
You should perhaps describe in more detail what you intend to
compare. While the chromosomes of a genome may be available as single
sequences, it's usually only single genes which are subjected to
multiple alignment.
Not quite true. There are alignments of whole genomes done for
finding syntenic blocks. These can be particularly useful when
looking for operons in bacterial genomes. For computational reasons,
they are done as pairwise alignments, but they are sometimes
interpreted as multiple alignments.
Doing synteny mapping for large genomes is a bit tricky, as it is easy
to be mislead by repeats. The UCSC genome browser group has done
several whole-genome alignments, including rat, mouse, human, chicken,
... , but not A. agrarius or C. glareolus. http://genome.ucsc.edu/
Their tools are available---you probably want to use BLAT, by Jim
Kent, though there may be other relevant tools.
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