new product: miraligner

[lorena.pantano]

We have released a beta version of a new product to mapping short
reads sequencing against miRBase database. You only need a fasta file
with reads. miraligner comes with miRBase repository (version 16.0),
but you can update easily to future upgrades.

Takes 15 second to map 19000 sequences allowing up to 1 mismatch. Also
no matching at the 3' end are allowed, up to 3 nucleotides. Only best
hits are reported and with full information about where they map and
the modification they have when comparing to the annotated miRNA.

Read the MANUAL.TXT file inside the package to know how to use it and
the main advantages. Go now to the Download section of the main web
page: http://estivill_lab.crg.es/seqbuster/

========================
QUICK START
========================

java -jar -Xms1000m -Xmx1000m miraligner/miraligner.jar 1 3 3 hsa
miraligner-1.0/test/test.fa miraligner-1.0/DB

Parameter 1: mismatches allowed (0/1)
Parameter 2: nucleotides allowed for trimming (max 3)
Parameter 3: nucleotides allowed for addition (max 3)
Parameter 4: species (3 letter, human=>hsa)
Parameter 5:fasta file
Parameter 6:folder where miRBase files are(one copy at miraligner-1.0/
DB folder)