Jim Mailman | 30 Oct 11:15 2014

[Biopython] Test feature location type

How to test Seqfeature location to know it's a Exact location, or non exact type, and know what type it is? Thanks, Jim

Biopython mailing list  -  Biopython <at> mailman.open-bio.org
Sanjeev Sariya | 24 Oct 20:10 2014

[Biopython] Understanding pdb biopython

Hi All,
I'm having a hard time using and understanding biopython pdb.
./read_pdb_file.py 3OE6.pdb

I'm attaching python script, pdb file, fasta file and output with mail.
I'have following doubts:
- When I print the sequence I get in broken pieces. Why?
- Also the sequence printed doesn't match with the fasta file (attached).
- Am I doing making a silly mistake?

I am running script as:
python read_pdb_file.py 3OE6.pdb 

Kindly help and guide.

Attachment (3OE6.pdb): invalid/x-pdb, 808 KiB
Attachment (read_pdb_file.py): text/x-python, 1018 bytes
Biopython mailing list  -  Biopython <at> mailman.open-bio.org
Ivan Erill | 24 Oct 17:34 2014

[Biopython] Faculty Position in Biological Data Science

Apologies for cross-posting

The Department of Biological Sciences at UMBC invites applications for a tenure-track Assistant Professor position in biological data science (i.e. bioinformatics, computational, theoretical or quantitative biology) specializing in computational neuroscience, metabolomics, metagenomics, data visualization or evolutionary genomics. The successful applicant will set up a computational laboratory and interact with faculty whose interests span the range from genomics and molecular genetics to evolution and behavior. Applicants must have a Ph.D. in a relevant field, post-doctoral experience in big-data computational or theoretical biology and a strong publication record, and are expected to establish a vigorous, externally funded research program, supervise doctoral-level graduate students, and teach at the undergraduate and graduate levels.

Applicants should submit a cover letter, curriculum vitae, research statement, research plan, a statement of teaching interests and philosophy and three letters of reference.  Application materials and letters of reference should be submitted to apply.interfolio.com/25756 by November 15, 2014.

UMBC is a medium-sized research university in the Baltimore-Washington D.C. area, whose combined excellence in research and outstanding educational programs have earned recognition by US News and World Report as the "#1 Up-and-Coming National University” for five years running. For information about the Department of Biological Sciences and its graduate programs, visit http://www.umbc.edu/biosci/.

The University of Maryland Baltimore County is an Equal Opportunity Employer/Affirmative Action. UMBC values gender, ethnic, and racial diversity; women, members of ethnic minority groups, and individuals with disabilities are strongly encouraged to apply. UMBC is the recipient of an NSF ADVANCE Institutional Transformation Award to increase the participation of women in academic careers.


Biopython mailing list  -  Biopython <at> mailman.open-bio.org
Thomas Girke | 22 Oct 19:09 2014

[Biopython] Faculty Position in Computational Systems Biology at UC Riverside

University of California, Riverside
AP Recruit job link: https://aprecruit.ucr.edu/apply/JPF00230

We are seeking an Assistant Professor in the field of Computational
Systems Biology. Research should be in systems biology, using
computational approaches or a combination of both experimental and
computational approaches.

Assistant Professor. Appointment and salary will be competitive and
commensurate with accomplishments.

University of California, Riverside.

The successful candidate will hold an academic appointment in the
Department of Botany and Plant Sciences with the option of a secondary
cooperating faculty appointment in a quantitative department such as
statistics, computer science, engineering or related. The candidate will
also join the innovative and multidisciplinary Institute for Integrative
Genome Biology (IIGB) which connects theoretical and experimental
researchers from different departments in Life, Physical and
Mathematical Sciences, Medicine, Engineering and various campus based
Centers. The IIGB is organized around a 10,000 sq.ft. suite of
Instrumentation Facilities that serve as a centralized, shared­use
resource for faculty, staff and students, offering advanced tools in
bioinformatics, microscopy, proteomics and genomics. Its bioinformatic
component is equipped with a modern high­performance compute (HPC)
infrastructure. This position will include an appointment in the
Agricultural Experiment Station, which incl udes the responsibility to
conduct research and outreach relevant to the mission of the California
Agricultural Experiment Station (http://cnas.ucr.edu/about/anr/).

A Ph.D. in a field related to systems biology is required including
several years of postdoctoral research.

Qualified candidates are expected to have excellent publication and
research records in computational systems biology or related areas, such
as bioinformatics or computational genome biology. The candidate’s
research program should be heavily focused on involving modern
high­throughput data, especially from next generation sequencing
technologies. An additional requirement is a strong commitment to
teaching in computational systems biology.

Review of applications will begin November 7, 2014 and continue until
the position is filled. Interested individuals should: (1) submit a
curriculum vitae, (2) provide a statement of research, and (3) three
letters of reference. A teaching statement is strongly recommended.
Please submit your applications through the AP Recruit job link:

Websites: http://www.genomics.ucr.edu, http://cnas.ucr.edu/, http://www.ucr.edu

The University of California is an Equal Opportunity/Affirmative Action
Employer/Veterans Employer. In accordance with Federal law, we are
making available our Campus Security Report to all prospective

Biopython mailing list  -  Biopython <at> mailman.open-bio.org
Ivan Gregoretti | 21 Oct 22:56 2014

[Biopython] Unix pipes and APIs like NcbiblastxCommandline()

Hello everybody

Can somebody suggest a way to run an API like NcbiblastxCommandline()
but directing the output to standard output?

For instance, this is the conventional execution with output directed
to a file, in this case opuntia.csv:

from Bio.Blast.Applications import NcbiblastxCommandline
blastx_cline = NcbiblastxCommandline("/mnt/shared/ncbi-blast-2.2.29+/blastx",
query="opuntia.fasta", db="nr", evalue=0.001, outfmt=10,

Now, what I would like to know is how to run this API with something like

out="/dev/stdout" instead of out="opuntia.csv".

In other words, I seek to avoid the creation of opuntia.csv.

Optional context:

I can currently execute local blast from within Python and direct its
output to a pipe (i.e. subprocess.Popen...). I am now interested in
trying the API way as it is likely to be more robust than my
implementation and already tested by a very large number of users.

Thank you,


Ivan Gregoretti, PhD
Biopython mailing list  -  Biopython <at> mailman.open-bio.org

Ivan Gregoretti | 20 Oct 21:08 2014

[Biopython] Running a specific version of NCBI BLAST from within Biopython

Hello Biopythoneers,

I have multiple versions of NCBI BLAST installed in my Linux box. I
need them all.

How do I tell Biopython which version of local BLAST I want to run each time?

Is it possible to specify the path to the desired executable?

Thank you,


Ivan Gregoretti, PhD
Biopython mailing list  -  Biopython <at> mailman.open-bio.org

Jaime Tovar | 17 Oct 15:05 2014

[Biopython] Using Phylo to draw trees with images in nodes

Hi all,

Sorry, seems my google fu is low today. Have been trying to find 
information about a way to add small images next to the species names in 
trees generated with Biopython/Phylo. But I'm not even sure it is 
possible. I want to do something in the likes of trees produced with 
ETE2. I can't use ETE2 because of problems with the dependencies :(.

Thanks in advance for any help!

Biopython mailing list  -  Biopython <at> mailman.open-bio.org

Mario Pavone | 17 Oct 12:49 2014

[Biopython] 1st announcement: Synthetic and Systems Biology Summer School: Biology meets Engineering and Computer Science, Taormina - Sicily, Italy July 5-9, 2015

Call for Participation (apologies for multiple copies)

Synthetic and Systems Biology Summer School: Biology meets Engineering  
and Computer Science - 2nd Edition
Taormina - Sicily, Italy, July 5-9, 2015

ssbss.school <at> gmail.com

** Deadlines **
Student Application: February 15, 2015
Oral/Poster Submission: February 15, 2015

The Synthetic and Systems Biology Summer School (SSBSS) is a  
full-immersion course on cutting-edge advances in systems and  
synthetic biology with lectures delivered by world-renowned experts.  
The school provides a stimulating environment for doctoral students,  
early career researches and industry leaders. Participants will also  
have the chance to present their results (Oral presentations or  
Posters) and to interact with their peers.

** Topics **
Genetic Engineering
Metabolic Engineering
Genome Design
Reading and Writing Genomes
Pathway Design
Synthetic Circuits and Cells
Biological CAD
Industrial Applications
Artificial Tissues and Organs
Genomically recoded Organisms
Biological Design Automation

** List of Speakers **
* Adam Arkin, University of California Berkeley, USA
* Jef Boeke, New York University, USA
* Angela DePace, Harvard University, USA
* Forbes Dewey, MIT, USA
* Paul Freemont, Imperial College London, UK
* Karmella Haynes, Arizona State University, USA
* Richard Kitney, Imperial College London, UK
* Timothy Lu, MIT, USA
* Philip Maini, Oxford University, UK
* Steve Oliver, Cambridge University, UK
* Greg Stephanopoulos, MIT, USA - TBC
* Nicola Zamboni, ETH, Switzerland

Other speakers will be announced soon.

** Industrial Panel **
* Zach Serber, Zymergen, Inc. USA

More speakers will be announced soon!

School Directors
Jef D. Boeke, New York University, USA
Giuseppe Nicosia, University of Catania, Italy
Mario Pavone, University of Catania, Italy
Giovanni Stracquadanio, University of Oxford, UK

** Short Talk and Poster Submission **
Students may submit a research abstract for presentation. School  
directors will review the abstracts and will recommend for poster or  
short-oral presentation. Abstract should be submitted by February 15,  
2015. The abstracts will be published on the electronic hands-out  
material of the summer school.


ssbss.school <at> gmail.com

Apologies for multiple copies. Please forward to anybody who might be  

To unsubscribe from this list, send a mail message (leaving the  
subject line blank) to cfp.ssbss <at> dmi.unict.it. The body of your  
message should contain the following one line: "unsubscribe your-email"

Dr. Mario Pavone (PhD)
Assistant Professor
Department of Mathematics and Computer Science
University of Catania
V.le A. Doria 6 - 95125 Catania, Italy
tel: 0039 095 7383038
fax: 0039 095 330094
Email: mpavone <at> dmi.unict.it
International Synthetic & Systems Biology Summer School
* Biology meets Engineering and Computer Science *
July 5-9, 2015 - Taormina, Italy
International Workshop on Artificial Immune Systems
* Systems & Synthetic Immunology, Computational Immunology,
          Immune-Inspired Engineering *
June 28-29, 2015 - Taormina, Italy
12th European Conference on Artificial Life - ECAL 2013
September 2-6, 2013 - Taormina, Italy

Biopython mailing list  -  Biopython <at> mailman.open-bio.org

Ivan Erill | 15 Oct 22:14 2014

[Biopython] WP_XXXXXXX RefSeq records

For bacteria, NCBI RefSeq is progressively adopting the non-redundant protein sequence standard. These protein records are aggregates for any bacterial genes coding for the same exact coding region (a "detailed" description of the implementation can be found here (ftp://ftp.ncbi.nlm.nih.gov/refseq/release/announcements/WP-proteins-06.10.2013.pdf).

Essentially, all traditional NP_XXXXXXX and YP_XXXXXXX protein records in bacteria RefSeq now map to a unique WP_XXXXXXX record. While this is possibly a good idea, it can create problems if one is trying to get back to (at least one of) the nucleotide sequence coding for the WP_XXXXXXX record.

For NP_XXXXXXX and YP_XXXXXXX records, one can easily fetch the protein record with Entrez.efetch, and then use the GB "coded_by" qualifier to access the corresponding nucleotide record.

Per specification of the new WP format:
- WP_ records will not include information about the corresponding Nucleotide sequences
on the sequence record.
- WP_ records will have links to Nucleotide in the Related Information section of the page display. Links in this section are available through NCBI’s E-utilities API.

I have been trying, unsuccessfully, to access the nucleotide record for WP_ proteins using Entrez.elink.

Here is an example:

Clicking on "Genomic records" in "Related information" will bring up the GenBank record containing the CDS for this protein, but I have been unable to use Entrez.elink to get to the information on the "Related information" panel. If I query:

handle = Entrez.elink(dbfrom="protein", id="653545797")

I essentially get an empty LinkSetDb. Any clues?

Biopython mailing list  -  Biopython <at> mailman.open-bio.org
Trevor Bell | 15 Oct 17:00 2014

[Biopython] Original BLAST query

I have run stand-alone BLAST of query sequences (Q1, Q2, Q3) against a set of reference sequences and written the results out in XML format, which I am then processing via BioPython. I am unable to find the original query sequences (Q1, Q2, Q3) in the XML file. Is this correct? When comparing each set of BLAST results, it would be useful to have access to the original query sequence, which was subjected to the BLAST, but this does not appear to be stored in the XML output.
Biopython mailing list  -  Biopython <at> mailman.open-bio.org
Naman Bhayani | 12 Oct 22:06 2014

[Biopython] Need Guidance to start contributing to BioPython

Hello sir,
 I am Naman,i study EEE,2nd year at BITS Pilani.
 I am relatively new to opensource contribution.I have started contributing since a few days and i am actively contributing BinPy organisation,and it participated in gsoc  2014.

My Github Profile: https://github.com/Rapternmn

My skills:C,C++,Python,Basic web development.
I am also interested in biology,so i thought it would be nice to explore and contribute to this organisation
I am willing to learn a lot more things.

Please tell me what do i need to know to start contributing to biopython and how should i begin contributing?

Thank you very much
Biopython mailing list  -  Biopython <at> mailman.open-bio.org