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insoedinglab/MMseqs2 (press backspace or delete to remove)MMseqs2 Clustering - Complete Command List (WSL)
1. Remove alignment gaps from the input FASTA
sed s/-//g /mnt/c/Users/file/Documents/aligned_codons.fasta /mnt/c/Users/file/Documents/no_gaps_sequences.fasta ...
Gumindu99
- 2
- Opened yesterday
- #977
Hi there, I am embarking on putting together a taxonomic database using MAGs with GTDB-style taxonomy annotations.
Specifically, I want to combine my MAGs with the current version of GTDB. To do that I ...
clb21565
- Opened 2 days ago
- #976
Hello, I m using the following command to find the closest references for multiple reads. As both the database and the
fasta file are quite big, it takes quite some time. I tried using max-seqs=7, however, ...
LauraVP1994
- Opened 3 days ago
- #975
Hi ！
I want to use MMseqs2 to obtain protein sequences from the query dataset that are completely dissimilar to the protein
sequences in the target dataset (e.g., with a similarity threshold of 0.3). ...
liyue9129
- 3
- Opened 7 days ago
- #973
Hi,
I started to use mmseqs2 to functionally annotate genes, and saw a surprising requirement of disk space. I tested the
swissprot db with a concatenated fna file using nohup mmseqs easy-search
/mnt/8T_2/zuo/gene_cluster_cohort/27_genes_cohort.fna ...
hellopeccat
- 2
- Opened 12 days ago
- #972
As instructed by the user manual and this blogpost, I used the following script to compute pairwise sequence identity
for a dataset (called bindingnet here):
fake_pref() {
QDB= $1
TDB= $2
RES= $3
...
wehs7661
- 4
- Opened 15 days ago
- #971
As far as I know, MMseq2 can be used instead of Blastn , and it has faster speed than Blastn . (even, two tools have
different usage) For understanding the algorithm of MMseq2, I was reading your paper, ...
JKL-uxf
- 1
- Opened 15 days ago
- #970
Hi there,
I have first downloaded nr.gz using mmseqs databases NR nr tmp, without any error found. However, when mmseqs2 went on
to automatically performed createdb tmp/18325772313164835411/nr.gz nr --compressed ...
- 6
- Opened 16 days ago
- #969
Hi, I wonder if it s possible to add a deduplication step before calculating MSAs for colabfold. I noticed that when
generating MSAs for a large batch of alphafold2-multimer-v3 analyses, there are quite ...
yanj14jy15
- Opened 22 days ago
- #968
Hi, thank you for the big work behind MMseqs2.
I tried to setup GTDB db (r220) as written in the WiKi. In the folder I successfully get all the files indicated by the
workflow:
taxonomy/
├── ar53_taxonomy_r220_reps.tsv ...
luigallucci
- 4
- Opened 24 days ago
- #967
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