User: martinsteinegger

Reputation:
30
Status:
New User
Location:
Last seen:
1 week, 1 day ago
Joined:
4 years ago
Email:
t******************@gmail.com

Posts by martinsteinegger

<prev • 4 results • page 1 of 1 • next >
0
votes
1
answer
357
views
1
answers
Comment: C: Missing GenBank identifier to NCBI taxonomy mapping
... Thanks a lot for your answer! This explains why I could not grep for the accession. However, I still do not know how to efficiently map the accessions to a taxonomical accession. I guess I need to query the project accession but this is a different problem. ...
written 10 months ago by martinsteinegger30
3
votes
1
answer
357
views
1
answer
Missing GenBank identifier to NCBI taxonomy mapping
... I have a problem to map GenBank identifiers to their NCBI taxonomical identifiers. I used the accession2taxid file (ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/) for the mapping. However out of my 400 million GenBank identifier only 150 million can be mapped to a taxonomical id. For example ...
ncbi taxonomy genbank written 10 months ago by martinsteinegger30 • updated 10 months ago by h.mon30k
0
votes
3
answers
614
views
3
answers
Answer: A: high-throughput domain discovery
... I am biased since I am the developers of [MMseqs2][1]. MMseqs2 can perform fast sequence/profile searches. It is possible to annotate 1.1 billion protein sequences with Pfam domains in 8.3 h on a 2×14-core server. [Here][2] is a guide how to setup the search. [1]: https://github.com/soedinglab/M ...
written 16 months ago by martinsteinegger30
2
votes
3
answers
2.4k
views
3
answers
Answer: A: Fast kmer reverse complement code using bit tricks
... We compute the reverse complement k-mer in [MMseqs2][1] using SIMD. The trick is to use two lookup tables (lookup1 and lookup2) for the reverse complements. The function should be roughly 1.3x times as fast as revcomp64_v2. It can probably still be optimized more. // Compute reverse complement ...
written 18 months ago by martinsteinegger30

Latest awards to martinsteinegger

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1506 users visited in the last hour