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wyp1125 / MCScanX

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
http://chibba.pgml.uga.edu/mcscan2/
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missing homologs #34

Open Everybody888 opened 3 years ago

Everybody888 commented 3 years ago

Hi, there, I found missing homologs in my results, though they show 100% homolog in my blastp results. I tried different parameters, checked all my command, nothing wrong, and I found this issue occurred more than 5 times in my overall results. Please help me solve this:

` 1 V.g1576 tig00000012_np1212.g1452
1 V.g1577 tig00000012_np1212.g1453
1 V.g1578 tig00000012_np1212.g1454
1 V.g1579 | |
1 V.g1580 | |
1 V.g1581 tig00000012_np1212.g1457
1 V.g1582 tig00000012_np1212.g1458
1 V.g1583 tig00000012_np1212.g1459

tig00000012_np1212.g1452 V.g1576 100.000 121 0 0 1 121 1 121 6.80e-86 243 tig00000012_np1212.g1453 V.g1577 100.000 129 0 0 1 129 1 129 1.98e-93 263 tig00000012_np1212.g1454 V.g1578 100.000 420 0 0 1 420 1 420 0.0 868 tig00000012_np1212.g1455 V.g1579 100.000 528 0 0 1 528 1 528 0.0 1078 tig00000012_np1212.g1456 V.g1580 100.000 530 0 0 1 530 1 530 0.0 1072 tig00000012_np1212.g1457 V.g1581 100.000 442 0 0 1 442 1 442 0.0 906 tig00000012_np1212.g1458 V.g1582 100.000 250 0 0 1 250 1 250 0.0 513 tig00000012_np1212.g1459 V.g1583 100.000 218 0 0 1 218 1 218 3.29e-157 432`

I used these commands: blastp -query JYF80.pp.fa -db Sc2.pp -out 80_Sc2.blast -evalue 1e-5 -num_threads 16 -outfmt 6 -num_alignments 5 MCScanX 80_Sc2 -e 1e-5 -s 10

EvoEcoImm commented 3 years ago

Hi there,

I have the same problem about missing homologs. Have you found a solution for this? Thanks.

Surbhigrewal commented 9 months ago

Did anyone work out a solution to this?