I haven't looked at the details of the phrap algorithm, but my understanding is that it makes many calls to cross_match for the alignments. We sped up RepeatMasker by replacing cross_match with WU-BLAST, so it may be possible to do the same with phrap. I've meant to look into this for a while, but it isn't anywhere near the top of my list. It depended quite a bit on the parameters, but we were able to increase speed by a factor of 30 without reducing sensitivity. There's a paper on the subject in Bioinformatics. The name of the program is MaskerAid, and since it is a generic cross_match bluffer, it might be easy to adapt it to phrap. But maybe not. If this is a topic of great interest, I could be convinced to take a closer look. The greatest potential time-sink is probably not hacking phrap, but doing the experiments to assess the differences in assemblies. -Ian On Sun, 23 Feb 2003, Ravi Kishore wrote: > Hello all, > > does anyone know about a parallel version of phrap. The version that i am > running is a single threaded one and its taking more than a week to finish > crunching the sequences . If there is a parallel version it would be of > great help as we have a 16 node cluster. > > Thanks > > ------------------------------------------ > Ravi K Makkena > # 211-1, Thorn Lane, > Newark , DE , 19711. > > ph 302 738 7861 (home) > 302 831 3183 (office) > > __________________________________________ > > _______________________________________________ > Biodevelopers mailing list > Biodevelopers at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biodevelopers >