BOL: Related items

Edanchin Lab

Thu, 19 Nov 2020 08:00:07 -0600

My main topics of interest are:

The impact of non tree-like evolution such as horizontal gene transfers and hybridization on species biology
Evolution and adaptation of animals in the absence of sexual reproduction and the underlying mechanisms
Genomic signatures of adaptation to a parasitic life-style

More at https://edanchin.org/

DeCoSTAR - Detection of Co-evolution

Jit — Fri, 14 Apr 2017 06:27:25 -0500

DeCoSTAR is a software which aims at reconstructing ancestral gene or genome organizations, in the form of sets of neighborhood relations -adjacencies- between pairs of ancestral genes or gene domains.
Ancestral genes or domains are deduced from reconciled gene trees in a context of birth, speciation, duplication, loss, transfer, which are either given as input or computed with the ecceTERA package, to which DeCoSTAR is integrated. DeCoSTAR constructs parsimonious scenarios of gains and breakages of adjacencies, and contains in particular all the features of previous software DeCo, DeCoLT, ArtDeCo and DeClone. It provides statistical supports on ancestral adjacencies, or the possibility to handle badly assembled genomes.
DeCoSTAR is able to reconstruct the histories of domains inside genes, including gene fusion and fission events, as well as ancestral genome structures for dozens of whole genomes from all kingdoms of life in a few minutes.

Address of the bookmark: http://pbil.univ-lyon1.fr/software/DeCoSTAR/

Genome Stability Laboratory

Mon, 07 Mar 2016 04:16:32 -0600

The bakers yeast, Saccharomyces cerevisiae is an ideal model organism to understand mechanisms of meiotic chromosome segregation. In S. cerevisiae and in mammals, the majority of meiotic crossovers are formed through a highly conserved MSH4p-MSH5p, MLH1p-MLH3p dependent pathway. We are interested in charactering the role of these complexes in crossover formation and distribution among all homolog pairs. Errors in this process are linked to congenital birth defects in humans such as Down's syndrome.Our laboratory is also interested in understanding the effect of genetic background on mutation rate variation using S. cerevisiae as a model. These studies are relevant for understanding cancer progression, genome evolution and architecture. We use high- throughput genomic methods as well as classical genetics to achieve these aims.

More at http://faculty.iisertvm.ac.in/~nishantkt/index.html

Katju Lab

Fri, 26 Feb 2016 03:25:32 -0600

TheLab seek to understand the genetic factors contributing to genomic variation and phenotypic diversity. To this end, we employ molecular and bioinformatic tools to study evolutionary processes at the level of populations, both experimental and natural, and genomes. Our research interests encompass a wide range of topics, including the evolution of organellar and nuclear genomes, gene duplication and the origin of novel function, and the fitness and phenotypic consequences of mutation in evolution. For details regards ongoing projects, please see the Research page.

http://katjulab.com/research.html

GeneValidator - Identify problems with predicted genes

Poonam Mahapatra — Fri, 26 Aug 2016 06:00:03 -0500

GeneValidator helps in identifing problems with gene predictions and provide useful information extracted from analysing orthologs in BLAST databases. The results produced can be used by biocurators and researchers who need accurate gene predictions.

If you would like to use GeneValidator on a few sequences, see our online GeneValidator Web App -http://genevalidator.sbcs.qmul.ac.uk.

If you use GeneValidator in your work, please cite us as follows:

Dragan M‡, Moghul MI‡, Priyam A, Bustos C & Wurm Y. 2016. GeneValidator: identify problems with protein-coding gene predictions. Bioinformatics, doi: 10.1093/bioinformatics/btw015.

Address of the bookmark: https://github.com/wurmlab/genevalidator

Gene Finding and Predictions

Poonam Mahapatra — Fri, 26 Aug 2016 07:26:27 -0500

In this exercise, a previously annotated gene will be used to measure the accuracy of different gene finding approaches. GRAIL, GENSCAN, geneid, FGENESH, GenomeScan, GrailEXP and GENEWISE will be used to annotate the sequence. Both search by signal, content and homology (protein and cDNA sequences) methods will be employed in order to improve the ab initio results. Weak conservation of Start codons will lead to wrong prediction of initial exons in most cases.

http://genome.crg.es/courses/Bioinformatics2003_genefinding/

Address of the bookmark: http://genome.crg.es/courses/Bioinformatics2003_genefinding/

DIAL

Abhimanyu Singh — Wed, 01 Mar 2017 08:42:28 -0600

A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to determine small insertions/deletions. Our main motivation is to use this tool to survey the genetic diversity of endangered species as the identified sequence differences can be used to design genotyping arrays to assist in the species' management.

http://www.bx.psu.edu/~ratan/

Address of the bookmark: http://www.bx.psu.edu/miller_lab/

Useful Bioinformatics Tools

Poonam Mahapatra — Mon, 29 Aug 2016 04:08:12 -0500

Collections of few handy tools for bioinformatician

http://molbiol-tools.ca/Convert.htm

Address of the bookmark: http://molbiol-tools.ca/Convert.htm

Desai Lab

Thu, 21 Apr 2016 10:21:07 -0500

Evolutionary Dynamics and Population Genetics

Natural selection and other evolutionary forces lead to particular patterns of evolutionary dynamics, and they leave characteristic signatures on the genetic variation within populations. We use a combination of theory and experiments to study the dynamics and population genetics of natural selection in asexual populations such as microbes and viruses.

We use both theory and experiments to study evolutionary dynamics and population genetics, particularly in situations where natural selection is pervasive.

http://desailab.oeb.harvard.edu/home

Prokka: tool for the rapid annotation of prokaryotic genomes

Jit — Mon, 06 Mar 2017 03:49:57 -0600

Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.

Address of the bookmark: http://www.vicbioinformatics.com/software.prokka.shtml