New release of GET_HOMOLOGUES

Dear users,
today we are announcing a new release of the GET_HOMOLOGUES package (20140110) that includes an updated version of compare_clusters.pl, which now performs as explained in the manual, including option -T for creating a parsimony pangenomic tree. The download links to get this code are as usual:

http://www.eead.csic.es/compbio/soft/gethoms.php

and

http://maya.ccg.unam.mx/soft/gethoms.php

Please let us know of any other bugs that you might encounter, we appreciate your comments,
many thanks,

Bruno Contreras and Pablo Vinuesa

Bioinformatician NGS Best Wishes for New Year

This year we didn't have Christmas greeting in the blog, and I received an email from Santa Claus asking for it. So we'll wish the best for New Year... (remember about the free NGS course in Zaragoza in January 2014)

Curso NGS en Zaragoza (30-31 Enero 2014)

Hola,
nuestro colega Miguel Pérez-Enciso impartirá los días 30-31 de Enero (30, mañana y tarde; 31, mañana) un curso básico de análisis de datos NGS en el Salón de actos de la facultad de veterinaria de la Universidad de Zaragoza, invitado y organizado por Luis Varona. El curso es gratuito y no requiere inscripción.

El horario será:
jueves   30: 11-14H y 16-18H
viernes  31: 10-13H


Si consigo un enlace con el material del curso lo pondré aquí, de momento no sé mucho más que lo que aparece en el propio material que Miguel usa (http://www.icrea.cat/Web/OtherSectionViewer.aspx?key=1403&titol=2012):

"This is a short introductory course for NGS analyses.
The course assumes no knowledge on NGS data or data analyses, rather to the contrary, if you have experience , you will be disappointed. It is not yet a hands-on course, I will rather present the material theoretically but I am open with help in the analyses. I assume you are a computer illiterate biologist but that you have realized that you need computers in daily life. You are willing to:

Analyze by yourself the data
Willing to learn linux and perl or similar (python ...)
The main topics covered are:
FASTQ format and sequence quality (Phred score and fastqc software)
A simple pipeline: BWA + Samtools
Visualization: IGV
Identifying SNPs: Samtools
Annotating SNPs: ensembl vep.pl
Identifying structural variants
RNAseq: tophat + cufflinks
Population genetics: pools and individuals
Association studies with sequence: IBSeq

All topics are treated at very beginners level and superficially (check accompanying slides)"

Feliz año a todos,
Bruno

ofertas de postdoc en Bioninformática (Dic2013)

Hola,
comparto información de ofertas de trabajo en bioinformática que nos han llegado, hasta luego,
Bruno

1.

"We are looking to recruit a young, post-doctoral researcher for work on: Development and application of bioinformatic analysis methods for identification of biomarkers to assess the efficacy of TGF-β RI inhibitors in vivo"

http://www.genxpro.info/contact_us/Open_Positions/

2.

"[..]The Computational Biology Group of the Luxembourg Centre for Systems Biomedicine seeks a highly-skilled Postdotoral Fellow to work on an exciting project on reconstruction and analysis of an integrated gene regulatory network model to elucidate key mechanisms of cellular reprogramming. The model will rely on the integration and mining of diverse transcriptomics and epigenomics data of different cell types from the Central Nervous System. The

Postdoctoral Fellow is expected to supervise a Ph.D. student working on this project. Both of them are expected to collaborate with other members of the CBG to develop a computational methodology aiming at designing, in-silico, cellular reprogramming events, with a focus on the nervous system. This project will be carried out in collaboration with Prof. Noel Buckley’s lab at Kings College London.

Requirements of the ideal candidate:
• Ph.D. degree in Bioinformatics, Computer Science, Biology or a related discipline
• Strong computational skills
• Prior experience in mathematical modelling of biological networks, especially in network inference and analysis
• Excellent working knowledge in English.

We offer:
• Full contract for three years with possibility of renewal
• Opportunity to supervise a Ph.D. student working on the project
• Opportunity to do applied research to medical problems within a highly dynamic research institution (LCSB) and in collaboration with internationally recognized partners
• An exciting international environment
• A very competitive salary

For further information, please contact:
Prof. Dr. Antonio del Sol
E-mail: antonio.delsol@uni.lu

Applications should contain the following documents:
• A detailed curriculum vitae
• cover letter mentioning the reference number
• description of past research experience and future interests
• name and addresses of three referees

All applications should be sent preferably in electronic version until December 31 st, 2013 to the following address:
Luxembourg Centre for Systems Biomedicine (LCSB)
University of Luxembourg
7, avenue des Hauts-Fourneaux
L-4362 Esch-sur-Alzette
Tel: +352-466644-6982 (Office)"

http://wwwen.uni.lu/lcsb/people/antonio_del_sol_mesa

GET_HOMOLOGUES for pan-genome analysis

Hola,

en el último número de Applied and Environmental Microbiology mi colega Pablo Vinuesa y yo publicamos un artículo describiendo el software GET_HOMOLOGUES, que tiene como abstract:

GET_HOMOLOGUES is an open source software package that builds upon popular orthology-calling approaches making highly customizable and detailed pan-genome analyses of microorganisms accessible to non-bioinformaticians. It can cluster homologous gene families using the bidirectional best-hit, COGtriangles or OrthoMCL clustering algorithms. Clustering stringency can be adjusted by scanning the domain-composition of proteins using the HMMER3 package, by imposing desired pair-wise alignment coverage cut-offs or by selecting only syntenic genes. Resulting homologous gene families can be made even more robust by computing consensus clusters from those generated by any combination of the clustering algorithms and filtering criteria. Auxiliary scripts make the construction, interrogation and graphical display of core and pan-genome sets easy to perform. Exponential and binomial mixture models can be fitted to the data to estimate theoretical core and pan-genome sizes, and high quality graphics generated. Furthermore, pan-genome trees can be easily computed and basic comparative genomics performed to identify lineage-specific genes or gene family expansions. The software is designed to take advantage of modern multiprocessor personal computers as well as computer clusters to parallelize time-consuming tasks. To demonstrate some of these capabilities, we survey a set of 50 Streptococcus genomes annotated in the Orthologous Matrix Browser as a benchmark case.

El  software  se puede descargar de http://www.eead.csic.es/compbio/soft/gethoms.php y también de http://maya.ccg.unam.mx/soft/gethoms.php y está escrito mayoritariamente en Perl, aunque contiene también trozos en R.

El manual del programa describe en detalle ejemplos de uso y está disponible en http://www.eead.csic.es/compbio/soft/manual.pdf .

Este paquete de programas se diseñó para el estudio de los pan y core-genomas de grupos de microorganismos, que es con lo que trabaja el grupo de Pablo fundamentalmente, y permite generar figuras como éstas:

Un saludo,

Bruno