Kevin Moran

Diamond and frameshifts in longer hits. Different results in Blastx vs Blastp [Bug]

2

Hello, I have an issue where diamond sometimes overlooks frameshifts when comparing longer queries against subjects. I am running the following command. diamond blastx -d test.dmnd -q input.fa -o test.txt...

Diamond returns longer queries than the targets it was mapped against.

1

Occasionally, diamond returns a hit longer than the sequences against which it was mapped. I.E. it extends beyond the reference region. Per my understanding this should be impossible. Top 3...

Diamond Clustering randomly crashing.

1

I'm using Diamond clustering as part of an alignment strategy. This means I can run clustering over millions of files across a dataset. I run 32 instances of diamond in...

diamond prepdb is no longer available

1

Attempting to call it on diamond v2.0.14.152 produces the following error. $ diamond prepdb -d orthosets/diamond/blast/Ortholog_set_M Error: Invalid command: prepdb. To print help message: diamond help

Motif finding in protein sequences.

3

Hello! What a wonderful program you have here. I was writing to ask if lightmotif is capable of searching for motifs in protein sequences. It looks like functionality is partially...

[Request] Align unaligned sequences to a profile

2

Would you consider adding an align to profile mode which will insert unaligned sequences into an existing alignment. Basically, akin to mafft's --add or --addfragments mode. Currently, I can jank...