September 13, 2009
Notes on JGAST use:
(1) JGAST is somewhere in between a local alignment algorithm (such as
BLAST) and a global alignment algorithm (such as CLUSTAL). If a query
sequence and a target sequence are on opposite strands, BLAST will
reverse one of the sequences so that both sequences are on the same
strand. CLUSTAL will not make this correction. In its current
iteration, JGAST does not make this correction. That is, JGAST
expects your query sequences to be in the same 5-3 orientation as
your target sequences. This will usually be true for 454
pyrosequencing (in which all the sequences will be in the same 5-3
orientation), but is not generally true for Sanger sequencing of a
clone library. I have code that will take 16S sequences and put them
all in the same 5-3 orientation. If you would like that code, let
me know (at email@example.com). If there is enough demand for
it, I will incorporate it into JGAST.
In summary, please ensure that if you use JGAST your query sequences
and target sequences are in the same 5-3 orientation.
(2) JGAST starts with a blast search and the blast results are stored
using BLASTs "-m 8" option. This is a tab delimited file. If your
FASTA file headers (the lines that start with ">") have tabs, and
those tabs get copied over to the BLAST output, this may confuse the
Java program that parses the BLAST output. Please ensure that there are no tabs in the headers of your FASTA file. I can send you code to purge your FASTA files of tabs. And if there is enough demand, I will add this code to JGAST.
If you have any questions, please contact me at firstname.lastname@example.org