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Microsatellites were searched using MISA [ 32] which identifies perfect, compound and interrupted microsatellite motifs.
SSRs were identified and localized using the software SSR Identification Tool SSRITT), which identifies perfect di-, tetra-,etra-, pentandand hexanucleotide repeats.
We examined this using clones which identified perfect matches in the sequence databases.
SSR motifs were identified using MISA 1.0 (MIcroSAtellite; http://pgrc.ipk-gatersleben.de/misa/) [ 51], which identifies both perfect and compound repeats.
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Compared with all the reported porcine miRNAs, we found that 230 miRNAs, including candidated novel miRNAs, which identified from this study had perfect matches with each other, and 120 had 1 or 2 base variations at the length of terminus.
Thus, to verify the correct prediction of CDS start codons, all inferred genes were aligned against the NCBI non-redundant database (nr database) using BLASTX [64], [65], which identified 233 entries as having no perfect match in the database.
Analysis was based on the MISA script, which identified di- to hexa-nucleotide repeat motifs (perfect and compound microsatellites) that are at least 12 bases in length.
Only reads with perfect matches to the genome data were retained, which identified between 268,717 and 748,568 unique mapped sequences for each library, representing 3.6-8.2 3.6-8.2 total millionreads (total 1).
BESs were used for mining the SSRs using Perl based MIcro SAtellite MISAA) http://pgrc.ipk-gatersleben.de/misa[ 19] search module which is capable of identifying perfect as well as compound SSRs.
