Algorithmic Biology Lab

Comparative genomic tool Sibelia 2.0 is here! With improved performance and new interactive circular visualization for web.

Lab members have met with members of Theodosius Dobzhansky Center for Genome BioInformatics at the St. Petersburg State University.

Details of the meeting.

You can download SPAdes 2.3 from http://bioinf.spbau.ru/spades, see new manual and the changelog.

Today is the first release of SiBELia — Synteny Block ExpLoration tool! It finds synteny blocks in genomes represented as nucleotide sequences using approach based on de Bruijn graphs.

Congratulation to Ilya Minkin — author of SiBELia and grad student at the St. Petersburg Academic Unviersity, and to Son Pham who is supervising this project. For more information please take a look at the poster. We'll be happy to hear your feedback.

20 сентября на на телеканале ТВЦ был показан репортаж про лабораторию алгоритмической биологии, а также другие научные и образовательные проекты Санкт-Петербурга.

We've ogranized and hosted RECOMB-AB (Open Problems in Algorithmic Biology) and RECOMB-BE (Bioinformatics Education) satellite conferences this year.

It was awesome to see you all in St. Petersburg, we'll post all materials and photos a little bit later.

Today we've also released first version of QUAST to public! QUAST is the ultimate tool to evaluate genome assemblies by computing various metrics (e.g., N50, number of ORFs, etc.), drawing plots and producing handy reports.

We use it every day to improve SPAdes single-cell assembler. Enjoy and we would be happy to hear your feedback.

We have just released new version of SPAdes 2.2 single-cell assembler!

Improvements of SPAdes 2.2 over previous versions:

• simplified installation process,
• decreased RAM usage (35 Gb instead of 85 Gb on E.coli single-cell dataset),
• increased speed (about three times faster),
• better results (larger N50, largest contig, number of found genes and others).

You can download SPAdes 2.2 from this page.

The lab have got two papers accepted to WABI this year. 12th Workshop on Algorithms in Bioinformatics will be held in Ljubljana (Slovenia) on September 10-12, 2012. The papers are:

• Nikolay Vyahhi, Son K. Pham, Pavel Pevzner. "From de Bruijn Graphs to Rectangle Graphs for Genome Assembly".
• Natalie E Castellana, Andrey Lushnikov, Piotr Rotkiewicz, Natasha Sefcovic, Pavel A Pevzner, and Adam Godzik, Kira Vyatkina. "MORPH-PRO: A Novel Algorithm and Web Server for Protein Morphing".

We've visited RECOMB-seq and RECOMB (16th Annual International Conference on Research in Computational Molecular Biology) in Barcelona! That was amazing conference, full of interesting people and fascinating talks on computational molecular biology, including our paper on PATH-SETS and Pavel's presentation of the SPAdes single-cell assembler. Most of the talks this year were focused on sequencing and genotyping technologies and algorithms, evolution, structural and functional genomics and molecular sequence analysis.

Just to remind, we'll hold the following RECOMB satellite conferences in St. Petersburg in August 2012:

• RECOMB Algorithmic Biology (AB), 27-29 August 2012.
• RECOMB Bioinformatics Education (BE), 26 August 2012.

We'll be glad to see you there.