labstructbioinf pLM-BLAST issues

labstructbioinf / pLM-BLAST

Detection of remote homology by comparison of protein language model representations

https://toolkit.tuebingen.mpg.de/tools/plmblast

MIT License

41 stars 5 forks source link

issues

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Memory requirements

#56 dc2211 closed 4 days ago
1
fix csv saving

#55 Argusmocny closed 1 week ago
0
emb files point to wrong direction

#54 dc2211 closed 6 days ago
2
[QUESTION/SUGGESTION] Determining realistic use cases and limitations

#53 DaRinker opened 3 weeks ago
1
[ERROR] "embeddings.py: error: unrecognized arguments: -proc 4"

#52 DaRinker closed 3 weeks ago
2
Duplicate indexes in a CSV file generated by the embeddings.py script

#51 staszekdh closed 1 week ago
0
Databases link

#50 Darius-Kazlauskas closed 3 weeks ago
1
Dev

#49 Argusmocny closed 2 months ago
0
47 return results of pre screening only

#48 Argusmocny closed 2 months ago
0
Return results of pre-screening only

#47 staszekdh closed 2 months ago
3
Add runcache

#46 Argusmocny closed 3 months ago
0
question about filling scoring matrix

#45 Chiyasa closed 4 months ago
3
Truncated alignments from self comparison

#44 staszekdh opened 5 months ago
0
adjust kernel size

#43 Argusmocny closed 5 months ago
0
kernel_size not adjusted automatically

#42 staszekdh closed 5 months ago
0
fix performence issue

#41 Argusmocny closed 6 months ago
0
rollback path threshold criteria

#40 Argusmocny closed 6 months ago
0
upd

#39 Argusmocny closed 7 months ago
0
Reduce duplicates

#38 Argusmocny closed 7 months ago
0
Reduce duplicates

#37 MiTRonGTE closed 8 months ago
0
add cuda support for `plmblast.py`

#36 MiTRonGTE opened 9 months ago
0
Small character default parameter mkdir bug fix

#35 MiTRonGTE closed 9 months ago
0
Small character bug fix

#34 MiTRonGTE closed 9 months ago
0
Dev workers

#33 staszekdh closed 9 months ago
0
Update pLM-BLAST on the MPI Toolkit

#32 staszekdh closed 5 months ago
0
Re-implement graphical display of database search results

#31 staszekdh opened 11 months ago
3
Redundant alignment shift

#30 KYQiu21 opened 11 months ago
2
Sequence names not in plmblast.py output

#29 seanrjohnson closed 9 months ago
4
Too large embedding files when using --asdir

#28 staszekdh closed 9 months ago
2
Multi-GPU support in embeddings.py

#27 staszekdh opened 11 months ago
3
18 example scan of a small genome

#26 MiTRonGTE closed 11 months ago
0
24 allow plmblastpy to use directories as query argument

#25 Argusmocny closed 11 months ago
0
allow `plmblast.py` to use directories as `query` argument

#24 Argusmocny closed 11 months ago
0
plmblast.py script doesn't work when following example

#23 seanrjohnson closed 7 months ago
16
dbtofile.py doesn't work for databases created from fasta files

#22 seanrjohnson closed 11 months ago
1
fix error for very small sequences in chunk cosine similarity

#21 Argusmocny closed 11 months ago
0
ERROR in function filtering_db

#20 staszekdh closed 11 months ago
0
UnboundLocalError: local variable 'outfile' referenced before assignment

#19 Citugulia40 closed 10 months ago
9
example scan of a small genome

#18 Argusmocny closed 11 months ago
0
Multi query feature

#17 Argusmocny closed 11 months ago
1
13 feature request faster and more robust database construction

#16 Argusmocny closed 12 months ago
0
#13 feature request faster and more robust database construction

#15 Argusmocny closed 1 year ago
0
added support for multiple queries

#14 MiTRonGTE closed 1 year ago
0
FEATURE REQUEST: faster and more robust database construction

#13 DaRinker closed 11 months ago
3
ERROR when using GPU: "ValueError('gpu is not available, but device is set to gpu and what now?')

#12 DaRinker closed 1 year ago
1
Error when making custom database "IndexError: list index out of range"

#11 DaRinker closed 1 year ago
1
"Multi-query input not implemented"

#10 DaRinker closed 11 months ago
15
Errors on creating a target dataset and searching against it.

#9 maovshao closed 1 year ago
6
Dev

#8 Argusmocny closed 1 year ago
0
readme update

#7 Argusmocny closed 1 year ago
0