Dear Aaron (or anyone else who knows), I've noticed that the SNP file format has changed in version 2.4.0 compared to what's mentioned here:
http://darlinglab.org/mauve/user-guide/files.html The first column is still "SNP pattern". But what use to be coordinates for each genome has now tripled. For each genome there is now: sequence_1_Contig sequence_1_PosInContg sequence_1_GenWidePos1 ... Would I be correct in saying that: 1) *_Contig is null if it contributes a gap to the SNP pattern. Otherwise, it gives the range of the contig. 2) *_PosInContg is 0 if it contributes a gap to the SNP pattern; otherwise, it is the position within that contig. 3) *_GenWidePos1 is 0 if it contributes a gap to the SNP pattern; otherwise it is the position within that genome. I'm thinking aloud a bit. :-) But it sounds like the old SNP file is just column 3. Is that correct? However, I'm a bit puzzled what contig means in this context. Does it refer to usage of the Mauve Contig Mover? That is, if MCM isn't used, then columns (2) and columns (3) are identical in value? (This is what I'm noticing and I'm trying to understand why...I think this is the reason, since I haven't used MCM.) Thank you! Ray ------------------------------------------------- This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
