User: Jose Manuel Duarte

Reputation:
270
Status:
Trusted
Location:
Zurich
Last seen:
1 year, 10 months ago
Joined:
4 years, 3 months ago
Email:
j************@gmail.com

Posts by Jose Manuel Duarte

<prev • 37 results • page 1 of 4 • next >
0
votes
2
answers
1.9k
views
2
answers
Answer: A: Reading FASTA with BioJava 4.0.0
... As Pierre says it is an issue with a missing dependency in your class path (log4j 2). You can get the jar manually and then point your eclipse project to it. However it is a lot easier and much more powerful to use maven to deal with the dependencies automatically.  BioJava is all set up already to ...
written 3.2 years ago by Jose Manuel Duarte270
0
votes
1
answer
1.3k
views
1
answers
Comment: C: The reason of multiple biounit files for one PDB
... In order to know whether a particular biounit comes from authors or PISA, you will need to look into the original PDB/mmCIF file. The biounit file only contains the result of applying the symmetry operators present in the REMARK 350 section (or the _pdbx_struct_oper_list field in mmCIF files) and do ...
written 3.5 years ago by Jose Manuel Duarte270
2
votes
1
answer
1.3k
views
1
answers
Answer: A: The reason of multiple biounit files for one PDB
... There's 2 main reasons for having multiple biounits in the PDB: When there are multiple equivalent copies of the biounit in the crystal, then they are annotated as several biounits. A very typical example would be 4re6: a dimeric protein with 4 chains in the asymmetric unit. In that example bioun ...
written 3.5 years ago by Jose Manuel Duarte270
0
votes
7
answers
6.4k
views
7
answers
Answer: A: Bio-Javascript?
... The BioJS project exists for quite some time now and aims mainly at visualisation of biological data. It has already quite a few components, like MSA viewer, tree viewer or protein feature viewer. I don't know the details but I suppose they must have developed a few common data structures, so I woul ...
written 3.5 years ago by Jose Manuel Duarte270
0
votes
6
answers
6.3k
views
6
answers
Comment: C: How To Extract Just The Coordinate Values From A Pdb File Converted To A Text Fi
... I would like to add that PDB files might look simple and thus it is tempting to write your own little parser like that above. In reality there are many subtle issues in the parsing that are best left to mature libraries to handle. Thus I'd recommend the use of Biojava too, see the tutorial ...
written 3.5 years ago by Jose Manuel Duarte270
0
votes
1
answer
903
views
1
answers
Answer: A: How to get list of atomic coordinates and atom names involed in solven accessibl
... You can do it programatically by using Biojava (from version 4). See for instance the tutorial or the demo. You will be able to do it with either PDB or mmCIF files as input. Thus it will work for even very large molecules. Note that since December 2014 the PDB has transitioned to mmCIF as the main ...
written 3.5 years ago by Jose Manuel Duarte270
2
votes
4
answers
4.6k
views
4
answers
Answer: A: List of bioinformatics journal with imapact factor around 1 and no publication f
... Impact Factors are hugely over-rated and it is widely acknowledged that they are a deeply flawed concept. They simply tell you what the average impact of other papers published in that journal is. That does not affect the quality or impact of your paper whatsoever. In my opinion the only thing you ...
written 3.8 years ago by Jose Manuel Duarte270
0
votes
0
answers
2.7k
views
0
answers
Comment: C: Pairwise sequence alignment with Biojava?
... Nope, 4.0 is not released yet. So you either wait until the release or get the sources from github which then will allow you to build locally 4.0.0-SNAPSHOT. Then you can use 4.0.0-SNAPSHOT in your pom ...
written 3.8 years ago by Jose Manuel Duarte270
0
votes
0
answers
2.7k
views
0
answers
Comment: C: Pairwise sequence alignment with Biojava?
... I've tried now with Java 8 and I can reproduce the problem when using BioJava 3.1. However using the current BioJava 4.0.0-SNAPSHOT seems to work fine. ...
written 3.8 years ago by Jose Manuel Duarte270
0
votes
0
answers
2.7k
views
0
answers
Comment: C: Pairwise sequence alignment with Biojava?
... Actually I've just seen this in the mailing list: http://mailman.open-bio.org/pipermail/biojava-l/2014-November/011339.html which looks very much like your error and then explains everything: the problem is with Java 8 (I tried with Java 7) ...
written 3.8 years ago by Jose Manuel Duarte270

Latest awards to Jose Manuel Duarte

Scholar 3.5 years ago, created an answer that has been accepted. For A: The reason of multiple biounit files for one PDB
Supporter 3.5 years ago, voted at least 25 times.
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Blastclust Has Been Depreciated. Does Anyone Know Why?
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Bioinformatics Journal with no publishing fees?
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Blastclust Has Been Depreciated. Does Anyone Know Why?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1750 users visited in the last hour