Open acpguedes opened 3 years ago
Actually, the 3rd column seems the index of the second column in the DB
>WP_013559137.1/75-347
142684 142684 552 1.00 3.074E-178 0 272 273 0 272 273 273M
>WP_100884676.1/127-401
176224 176224 556 1.00 1.444E-179 0 274 275 0 274 275 275M
176224 25526 450 0.816 6.976E-143 0 260 275 0 260 261 261M
176224 29929 445 0.816 2.233E-141 0 260 275 0 260 261 261M
176224 139077 440 0.804 1.839E-139 1 261 275 0 260 261 261M
176224 102797 439 0.800 3.454E-139 1 260 275 0 259 260 260M
176224 76310 214 0.405 1.851E-61 15 273 275 6 259 260 159M5I95M
176224 117250 209 0.412 1.487E-59 12 273 275 3 259 260 162M5I95M
176224 131144 212 0.400 1.213E-60 9 268 275 4 258 260 165M5I90M
alignall
doesn't actually create a real alignment database, it's first two columns are 1) query key, 2) target key instead of 1) target key. convertalis
doesn't really now what to do with it. We didn't need this functionality yet, so it's kind of unfinished.
What is the overall purpose of this functionality? Perhaps I may help to dev in my free time.
Inside one cluster it produces alignment results for all possible pairs.
Ah I forgot the Needleman-Wunsch part of your question. We don't use global alignments basically anywhere. For proteins everything is smith-waterman and for nucleotides the banded alignment algorithm is a global one, but used in a way to compute local alignments.
If you are interested to work on this:
You should replace the currently used DB type Parameters::DBTYPE_GENERIC_DB
in alignall
with a new one. And then in convertalis
check if it's a normal alignment database or this new database type and introduce some special case to deal with the presence for both a query and target key.
Ok, I'll play with it. I'll keep you updated on any progress. Thanks
Hi,
This is more of a question than an issue.
I was playing around with
mmseqs alignall
intending to see how it works. I think maybe it is in development.I took a cluster I had and run
alignall
followed bycreatetsv
andresult2flat
.1- I didn't found how to extract the alignments in fasta format 2- the TSV has many different alignments with the same pairs 3- the FLAT has a fasta header with the representative sequence followed by the same type of table I got in TSV
It seems that it doesn't run a global alignment as Needleman-Wunsch. There is a way to do this all-vs-all with the Needleman-Wunsch algorithm? Also, there is a way to extract the sequences? I know I may process it using the CIGAR format reported in the TSV. And the last question, what is the 3rd column in the tsv?
Finally, very interesting new useful applications, thanks. Greets