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Dias de Bioinfo
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Movidos pela visita de alguns pesquisadores do grupo Helix do
INRIA (França), que forma com o DCC-IME-USP uma equipe associada,
o grupo de Bioinfo e o grupo de Combinatória do IME estão
organizando alguns dias de palestras na área de Bioinformática.
Do lado francês, teremos quatro palestras.
Do lado brasileiro, teremos algumas palestras curtas, de apresentação,
num dia da semana da Pátria a ser divulgado durante a próxima semana.
As palestras da semana que vem são:
Terça, dia 30 de agosto, das 16 as 17:30.
Marie-France Sagot, das 16:00 às 16:45
Pierre Peterlongo, das 16:50 às 17:30.
Um café com bolachas será servido entre as duas palestras.
Quarta, dia 31 de agosto, das 14 as 15:30.
Christian Gautier, das 14:00 às 14:45
Leonor Palmeira, das 14:50 às 15:30.
Um café com bolachas será servido entre as duas palestras.
As palestras ocorrerão no anfiteatro Gilioli, no Bloco A.
Os resumos seguem abaixo.
Todos são bem-vindos!!
Alan, Carlinhos e Cris
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Esta atividade faz parte do
Projeto INRIA/FAPESP 04/14335-5 Algorithmic Questions on Molecular
Biology e da Equipe Associada INRIA/USP Computational biology,
algorithmics, combinatorial optimization.
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Título: The life of a BAOBAB in Lyon, France
Palestrante: Marie-France Sagot
Ex BCC-IME student (class of 91)
BAOBAB-HELIX team
INRIA-LBBE (UMR 5558), Lyon, France
This talk will present an overview of the research activities of the
BAOBAB team. It will also serve to place in context three other talks
from members of the team that will follow this one, one the same day
and two the day after.
The BAOBAB team is part of two distinct bigger French research
structures, the HELIX project of the INRIA, the national institute of
research in computer science, and the "Laboratoire de Biometrie et
Biologie Evolutive" (LBBE) which is a laboratory affiliated to both
the CNRS and the "Universite Claude Bernard" (Lyon I). The LBBE is
composed mainly of biologists, bio-mathematicians and
bio-informaticians.
The BAOBAB team mirrors this multidisciplinarity in a perhaps starker
way. Its members come thus from mathematics, statistics, (theoretical)
computer science and biology (molecular biology, evolution,
biochemistry). The team has a number of objectives that reflect its
varied backgrounds yet common passion for biology.
Through it's head, the team has been collaborating with the IME for
many years. Since January of this year, the DCC-IME is an official
research partner of BAOBAB-HELIX, with support from both the INRIA and
the FAPESP for developing its collaboration. It is in the context of
this partnership that the talks and visits of seven members of BAOBAB
to the IME are taking place.
For more information on the activities of BAOBAB, you may consult:
http://www.inrialpes.fr/helix/people/sagot/team/index.html
For information on the partnership between BAOBAB and the DCC-IME,
you may consult:
http://www.inrialpes.fr/helix/people/sagot/team/projects/associated_team_usp_helix/associated_team_usp_helix.html
PS: BAOBAB stands for "Biologie et Algorithmie Ou Bien Algorithmie
et Biologie".
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Título: Lossless Filter for Finding Long Multiple Approximate
Repetitions Using a New Data Structure, the Bi-Factor Array
Palestrante: Pierre Peterlongo
IGM-BAOBAB
Universite Marne-la-Vallee, Paris, France
Similarity search in texts, notably biological sequences, has received
substantial attention in the last few years. Numerous filtration and
indexing techniques have been created in order to speed up the
resolution of the problem. However, previous filters were made for
speeding up pattern matching, or for finding repetitions between two
sequences or occurring twice in the same sequence. In this talk, we
present an algorithm called NIMBUS for filtering sequences prior to
finding repetitions occurring more than twice in a sequence or in more
than two sequences. NIMBUS uses gapped seeds that are indexed with a
new data structure, called a bi-factor array, that is also presented
in this paper. Experimental results show that the filter can be very
efficient: preprocessing with NIMBUS a data set where one wants to
find functional elements using a multiple local alignment tool such as
GLAM, the overall execution time can be reduced from 10 hours to 6
minutes while obtaining exactly the same results.
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Título: Similarity between neighbors: selection or mutational bias
inside genomes?
Palestrante: Christian Gautier
BAOBAB team
LBBE (UMR 5558), Lyon, France
In all three biological worlds (eukaryotes, prokaryotes, archea) it
appears that neighbor sequences (genes or non coding sequences) are
more similar than random ones. These similarities are very diverse and
can involve base frequencies, transcription direction, expressivity,
etc. An important evolutionary question is "what are the mechanisms
that create and maintain such regional similarities?" As very often,
the debate between natural selection and mechanistic effects of genome
functioning appears and some relevant mathematical analysis from the
lab are presented.
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Título: Dinucleotide over- and under-representation in complete
bacterial genomes (Bacteria and Archaea)
Palestrante: Leonor Palmeira
BAOBAB team
LBBE (UMR 5558), Lyon, France
Statistical analysis of the representation of oligonucleotides has
been widely used to try and shed light over sequence structure -- to
try and determine the degree in which randomness and selection play a
part within biological sequences. In order to understand these
features, we conducted a systematic study of the over- and
under-representation of dinucleotides in completed Bacteria and
Archaea genomes. In this talk, we will first present the general
statistical methodology used. We will then discuss some main results.
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