User: Alex Richter

gravatar for Alex Richter
Alex Richter210
Reputation:
210
Status:
Trusted
Location:
San Diego
Last seen:
1 year, 1 month ago
Joined:
9 years, 9 months ago
Email:
r*********@gmail.com

Bioinformatics Engineer at J. Craig Venter Institute. Currently doing altogether too much grid (SGE) and hadoop hacking. JAPH

Posts by Alex Richter

<prev • 9 results • page 1 of 1 • next >
0
votes
1
answer
2.0k
views
1
answers
Comment: C: Is it possible to extract the reference sequence from the BWA index files?
... Thanks! Since I hopefully won't need to do this much, I'll do what you suggest, and munge in the annotations. ...
written 4.3 years ago by Alex Richter210
9
votes
1
answer
2.0k
views
1
answer
Is it possible to extract the reference sequence from the BWA index files?
... I have a series of BWA index files ( *.amb *.ann *.bwt, etc) but the original reference fasta sequences are not available. Assuming that it's a complete burrows-wheeler index, the complete reference should be encoded in those indices. Does anyone know if/how the fasta can be re-extracted from them? ...
alignment bwa written 4.3 years ago by Alex Richter210 • updated 4.3 years ago by matted7.3k
2
votes
2
answers
3.3k
views
2
answers
Answer: A: Velvetg: 'Killed' During ___/___ Nodes Visited
... In general, if you are running a program in Linux, and it exits with a 'Killed' message (and assuming that you haven't kill -9'd it yourself), it means that either you hit the ulimit (as per Istvan's comment above), or that the kernel was forced to kill it due to running out of memory (both physical ...
written 8.7 years ago by Alex Richter210
0
votes
5
answers
4.1k
views
5
answers
Comment: C: Parse A Embl Like Format To Fasta Format
... Hmm. That error normally only occurs when you attempt to assign a value to a reference (e.g. $/ = "//n"; ) If you can show me lines 3-5, I might have a better idea. ...
written 9.0 years ago by Alex Richter210
1
vote
5
answers
4.1k
views
5
answers
Answer: A: Parse A Embl Like Format To Fasta Format
... How about this? It's remarkably hacky, but should do the trick. #!/usr/bin/env perl use strict; use warnings; $/ = "//\n"; while (<>) { chomp; my %record; foreach my $line (split /\n/) { my ($key, $val) = unpack("A4A*", $line); $record{$key} .= $val; } prin ...
written 9.1 years ago by Alex Richter210
5
votes
1
answer
1.5k
views
1
answers
Answer: A: Inheritance Question In Bioperl
... This is not so much a Bioperl question as an inheritance one. You will need to write a constructor which takes a `BSF::G` and returns your object. It will look something like sub new_from_generic { my $class = shift; my $generic = shift; my $self = bless($generic, $cla ...
written 9.6 years ago by Alex Richter210 • updated 9 months ago by RamRS27k
0
votes
3
answers
3.3k
views
3
answers
Comment: C: Tigr Functional Assignment Using Cdd And Rps-Blast
... Unfortunately for denim, they are using the CDD translations of the TIGRFAM HMMs. Searching against TIGRFAMs directly via hmmpfam (version 2, still) would be a good way to use these (manually curated, BTW) cutoffs, but the scale changes completely when you move to PSIblast profiles. As Kader mention ...
written 9.6 years ago by Alex Richter210
0
votes
1
answer
3.2k
views
1
answers
Comment: C: How Can I Convert Hmmer Hmm Descriptions To Psi-Blast Pssms?
... Looks interesting, although it's missing a couple columns in the PSSM, and I'm not entirely sure where the `$your_query_sequence` is coming from. I'll have to see if I can get it to work. If nothing else, it'll give me a place to start. ...
written 9.7 years ago by Alex Richter210 • updated 9 months ago by RamRS27k
15
votes
1
answer
3.2k
views
6 follow
1
answer
How Can I Convert Hmmer Hmm Descriptions To Psi-Blast Pssms?
... I'm attempting to generate an rpsblast database from a set of protein cluster alignments. For most of them, I could use blastpgp -B <alignment> to generate the PSSM without problem, but several of the alignments (namely the large ones, or the ones with huge sequences) crash (seg-fault) blastpg ...
hmm written 9.7 years ago by Alex Richter210 • updated 9.7 years ago by Niek De Klein2.5k

Latest awards to Alex Richter

Popular Question 3.3 years ago, created a question with more than 1,000 views. For Is it possible to extract the reference sequence from the BWA index files?
Student 3.3 years ago, asked a question with at least 3 up-votes. For Is it possible to extract the reference sequence from the BWA index files?
Popular Question 6.1 years ago, created a question with more than 1,000 views. For How Can I Convert Hmmer Hmm Descriptions To Psi-Blast Pssms?
Appreciated 6.5 years ago, created a post with more than 5 votes. For A: Inheritance Question In Bioperl
Appreciated 6.5 years ago, created a post with more than 5 votes. For How Can I Convert Hmmer Hmm Descriptions To Psi-Blast Pssms?
Good Question 6.5 years ago, asked a question that was upvoted at least 5 times. For How Can I Convert Hmmer Hmm Descriptions To Psi-Blast Pssms?
Teacher 6.5 years ago, created an answer with at least 3 up-votes. For A: Inheritance Question In Bioperl
Student 6.5 years ago, asked a question with at least 3 up-votes. For How Can I Convert Hmmer Hmm Descriptions To Psi-Blast Pssms?
Autobiographer 6.5 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1417 users visited in the last hour