User: Tim

gravatar for Tim
Tim320
Reputation:
320
Status:
Trusted
Location:
Nijmegen, the Netherlands
Last seen:
6 years, 9 months ago
Joined:
9 years, 5 months ago
Email:
t********@gmail.com

Posts by Tim

<prev • 22 results • page 1 of 3 • next >
0
votes
6
answers
11k
views
6
answers
Comment: C: Is There A List Of Public Galaxy Servers?
... The team behind the NBIC Galaxy instance you linked too are working on setting up a RPM repository for tools they have added to their instance.. For details see: https://wiki.nbic.nl/index.php/NBIC_%26_VIB_Bioinformatics_RPM_Repository ...
written 8.2 years ago by Tim320
1
vote
11
answers
11k
views
11
answers
Answer: A: Is Amazon'S Ec2 Commonly Used For Bioinformatics?
... QIIME offer their pipeline for microbial community analysis as an EC2 image. ...
written 8.4 years ago by Tim320
0
votes
6
answers
7.0k
views
6
answers
Comment: C: How To Extract Just The Coordinate Values From A Pdb File Converted To A Text Fi
... Thanks for trying to help, but he was asking for a Java only solution.. (Although I wasn't the one who gave you the downvote) ...
written 8.4 years ago by Tim320
2
votes
2
answers
6.6k
views
2
answers
Answer: A: Predicting Effect Of Single Mutation On Protein Structure
... Not to toot my own horn, but is sounds like http://www.cmbi.ru.nl/hope/home well suits your needs, provided homologs are available to build a homology model. Just enter your sequence & mutation, wait for the model to be build, and you'll get a human readable report detailing the effects on the ...
written 8.4 years ago by Tim320
0
votes
1
answer
3.9k
views
1
answers
Comment: C: Error Translating Genbank Cds Using Biopython
... Thanks for the explanation, and about the provided translation: I'll discuss again with my supervisors if I can use the already provided translation in when encountering /transl_except records. I think writing my own code to handle the /transl_except cases is far more error-prone than using the prov ...
written 8.4 years ago by Tim320
0
votes
3
answers
19k
views
3
answers
Comment: C: Correct Method To Blast All-Vs-All With Ncbiblast & How To Speed It Up?
... I'll probably have to move in this direction as I was indeed already using the tabular output (-outfmt 6 in the newest blast version). ...
written 8.4 years ago by Tim320
10
votes
3
answers
19k
views
8 follow
3
answers
Correct Method To Blast All-Vs-All With Ncbiblast & How To Speed It Up?
... Hi all, I'm using ncbi-blast-2.2.24+ (on Ubuntu linux) for a sizable all-vs-all blast of protein sequences (530.000 lines of fasta). This is taking quite a while (over an hour) already, so I'm looking into ways to speed it up. What I've done is run: ncbi-blast-2.2.24+/bin/makeblastdb -in good_pro ...
blast written 8.4 years ago by Tim320 • updated 6.1 years ago by jsporter60
0
votes
1
answer
3.9k
views
1
answers
Comment: C: Error Translating Genbank Cds Using Biopython
... Thanks, this seems like a good method to fall back upon. I was hoping there was some oversight on my side of a way to handle this case using BioPython, as I've seen quite a few people running into similar problems while Googling: BioPython transl_except. Any suggestions in that direction are still w ...
written 8.4 years ago by Tim320
5
votes
1
answer
3.9k
views
1
answer
Error Translating Genbank Cds Using Biopython
... Hi all, I'm trying to translate the a genbank record using BioPython 1.53, ignoring the already given translation in the CDS feature. The code I've written to translate this is pretty straight forward: ... for gb_record in SeqIO.parse(file_handle, 'genbank'):#Bio.GenBank.Record for gb_feature ...
translation biopython genbank written 8.4 years ago by Tim320 • updated 5.5 years ago by Biostar ♦♦ 20
1
vote
5
answers
3.2k
views
5
answers
Answer: A: How To Study Effects Of Mutations
... Since you've added the protein tag I thought I'd link this: http://www.cmbi.ru.nl/hope/home It studies the structural & functional effects of a single protein point mutation fully automatically and displays a readable report with illustrations, which could be a nice start off point for further a ...
written 8.5 years ago by Tim320

Latest awards to Tim

Supporter 6.8 years ago, voted at least 25 times.
Popular Question 8.4 years ago, created a question with more than 1,000 views. For Correct Method To Blast All-Vs-All With Ncbiblast & How To Speed It Up?
Teacher 8.8 years ago, created an answer with at least 3 up-votes. For A: Amino Acid Residues Changes/Mutation Causing Diseases
Appreciated 9.0 years ago, created a post with more than 5 votes. For Create Structure Image From Inchi
Student 9.0 years ago, asked a question with at least 3 up-votes. For Create Structure Image From Inchi
Appreciated 9.5 years ago, created a post with more than 5 votes. For Score Protein Variants Based On Frequency Of Aa In Multiple Sequence Alignment
Student 9.5 years ago, asked a question with at least 3 up-votes. For Score Protein Variants Based On Frequency Of Aa In Multiple Sequence Alignment

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 851 users visited in the last hour