This script takes as input a series of sequences (we have used the entire pool of putatively single-copy markers developed by the 1KP project - www.onekp.com), blasts each of these putatively single-copy sequences against the pool of transcriptomes and then takes the resulting hits and blasts them against the transcriptomes again. From this final pool of hits lasseblaste produces an alignment based on all the sequences produced from each of the queries, using MAFFT (Katoh, 2002), and provides a quality score for each of these alignments (the score rewards alignments that have broad representation across transcriptomes indicating good taxon coverage, and penalizes alignments that have many hits per transcriptome, indicating multiple paralogs or short read lengths). We selected the five best-scoring of these alignments to pursue for primer design.
the script is distributed in a zip-file as a complete maven-java-project
Anders Larsson,
Dep. of Systematic Biology
Uppsala University
Sweden
email: anders.larsson [at] ebc.uu.se
Phone: +46 (0)18 471 2932
Fax: +46 (0)18 471 6457