Brief description of output columns? about foldseek

[milot-mirdita]

Essentially its the same format as described here:
https://github.com/soedinglab/MMseqs2/wiki#custom-alignment-format-with-convertalis

However, in TMalign mode, evalue and bitscore are both TMscore.

[rezahay]

Thanks for your quick response. The output file contains multiple records such as:

job.pdb AF-P0A1G5-F1-model_v2.pdb.gz 100.000 41 0 0 1 41 111 151 6.180E-05 209 41 151 FGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREKQMAG FGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREKQMAG -8.680,37.207,21.983,-9.232,34.623,19.132,-6.462,34.101,16.601,-7.603,30.809,15.047,-4.576,28.764,13.940,-5.145,28.262,10.189,-3.572,24.760,9.805,-2.046,24.647,6.287,-3.639,21.502,4.799,-0.804,20.174,2.623,-2.098,19.840,-0.977,-0.437,16.358,-0.744,-2.991,15.032,1.816,-5.168,12.055,0.679,-8.229,14.155,1.703,-7.154,17.029,-0.617,-6.738,14.552,-3.562,-10.300,13.315,-2.921,-11.776,16.858,-2.471,-13.106,15.725,0.959,-13.102,17.329,4.416,-12.379,15.266,7.589,-15.460,13.246,8.674,-17.324,14.581,11.733,-18.419,11.675,13.972,-21.823,12.190,15.665,-22.359,11.053,19.308,-23.729,7.452,19.214,-23.142,7.014,15.449,-22.756,3.358,14.380,-19.219,2.542,13.198,-18.939,1.957,9.403,-22.452,3.081,8.510,-23.317,3.812,4.828,-22.197,7.491,5.160,-18.755,6.491,6.585,-18.271,3.726,3.953,-19.261,6.191,1.156,-16.721,8.710,2.566,-13.849,6.148,2.541,-14.925,4.772,-0.889,-14.644,8.307,-2.386,-11.183,8.740,-0.782,-9.893,5.333,-2.001,-11.281,5.813,-5.568,-9.837,9.345,-5.923,-6.457,8.189,-4.537,-6.461,5.115,-6.868,-7.240,7.327,-9.902,-4.496,9.874,-9.011,-1.935,7.021,-8.604,-3.012,5.583,-12.022,-2.537,9.000,-13.687,0.937,9.259,-12.024,1.974,5.756,-13.222,0.781,6.588,-16.794,2.755,9.918,-16.767,5.923,8.166,-15.485,5.587,5.492,-18.234,5.355,8.289,-20.866,8.410,10.084,-19.351,10.471,6.837,-19.320,9.526,6.237,-23.019,10.674,9.768,-23.993,13.970,9.296,-22.043,14.552,5.890,-23.729,14.081,7.551,-27.179,16.871,10.089,-26.342,20.397,8.609,-26.559,22.538,10.284,-23.830,26.093,11.471,-24.436,28.741,9.017,-23.017,29.348,11.410,-20.035,25.611,11.712,-19.111,24.674,8.005,-19.650,25.500,7.129,-16.010,23.222,9.906,-14.623,20.299,8.964,-16.941,20.655,5.226,-16.038,20.564,6.145,-12.292,17.423,8.340,-12.759,15.674,5.659,-14.873,16.499,3.030,-12.184,14.901,5.238,-9.461,11.765,5.914,-11.579,11.409,2.168,-12.325,11.625,1.308,-8.563,9.124,4.051,-7.585,6.617,2.987,-10.305,6.785,-0.635,-9.054,5.975,0.634,-5.478,3.020,2.718,-6.804,1.664,-0.340,-8.715,1.858,-2.375,-5.450,0.071,0.497,-3.635,-2.718,0.600,-6.324,-3.229,-3.189,-5.826,-3.374,-2.560,-2.040,-6.021,0.201,-2.521,-8.038,-2.157,-4.813,-7.878,-4.836,-2.048,-9.064,-2.180,0.473,-11.933,-1.097,-1.872,-13.115,-4.756,-1.872,-13.175,-4.679,1.983,-15.395,-1.541,1.747,-17.739,-3.405,-0.686,-17.759,-6.549,1.556,-18.621,-4.391,4.691,-15.350,-5.688,6.398,-13.648,-2.244,6.349,-12.303,-0.342,9.393,-11.420,-3.264,11.743,-7.962,-4.467,12.865,-7.042,-7.791,11.130,-5.113,-8.897,14.309,-7.547,-8.106,17.184,-10.928,-7.069,15.620,-10.768,-3.587,17.288,-12.137,-0.580,15.343,-9.541,1.600,13.594,-10.333,5.234,14.496,-11.820,7.288,11.593,-9.061,9.977,11.675,-6.457,7.168,11.348,-8.237,5.713,8.283,-8.433,9.269,6.786,-4.662,9.639,7.270,-4.089,6.109,5.827,-7.205,4.359,4.389,-5.180,1.177,3.547,-4.450,0.531,7.282,-4.979,-3.180,8.179,-3.971,-3.081,11.920,-4.844,-0.869,14.960,-2.065,1.455,16.299,-1.059,-1.033,19.055,-0.890,-4.116,16.769,1.002,-2.040,14.139,3.526,-0.835,16.783,4.024,-4.419,18.071,4.538,-5.640,14.462,7.248,-2.943,13.886,9.028,-3.871,17.181,8.992,-7.580,16.126,10.255,-6.666,12.609,13.282,-4.810,14.133,14.053,-7.781,16.454,13.768,-10.443,13.673,15.546,-8.511,10.851,18.808,-7.977,12.855 MQEGQNRKTSSLSILAIAGVEPYQEKPGEEYMNEAQLSHFKRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERKLIKKIEKTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREKQMAG 99287 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

which seems to be different than:
targetID alnScore seqIdentity eVal qStart qEnd qLen tStart tEnd tLen [queryOrfStart] [queryOrfEnd] [dbOrfStart] [dbOrfEnd] [alnCigar]

I know these columns (of mmseqs2) but the above record is different. Would you please give me a hint how should I interpret the columns of the above record?

[milot-mirdita]

The api m8 has additional columns to enable all the stuff in the web visualization:
The first twelve are the normal output:
query,target,pident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits
Then we add the sequence lengths, alignments and target C-alpha cooridnates:
qlen,tlen,qaln,taln,tca,tseq
And if a db with taxonomy information was searched we add also this information:
taxid,taxname

[ronboger]

@milot-mirdita it seems like there's a missing column between tend and evalue, as there are 21 columns. Do you have insight on what it may be?

[milot-mirdita]

See my answer in the other thread:

We recently added the Foldseek match probability (prob).
Also we return pident not fident and since recently for some of the databases theader instead of target to get the full header.