[Cascavel-pm] Fwd: [perlbr] Estágio remunerado: projeto de Bioinformática

fglock em pucrs.br fglock em pucrs.br
Domingo Dezembro 12 21:46:37 CST 2004

Forwarded Message:
> To: perlbr em yahoogrupos.com.br
> From: "amrdavila" <amrdavila em yahoo.com>
> Subject: [perlbr] Estágio remunerado: projeto de
> Date: Sun, 12 Dec 2004 18:44:37 -0000
> -----
> Estágio remunerado. Procura-se 1 ou 2 programadores
que saibam
> Perl, CGI e MySQL para trabalhar por 1-2 meses num
projeto na área
> de Bioinformática. Local de trabalho: Fundação
Oswaldo Cruz
> (RJ).
> Início das atividades : primeira semana de janeiro
de 2005. Podem
> se candidatar programadores que tenhma segundo
grau, estudantes de 
> curso superior e inclusive formados. Para
candidatos com interesse 
> acadêmico, existe também a possibilidade de bolsa de
> iniciação científica do CNPq.
> Interessados devem enviar CV resumido para o email
amrdavila AT 
> yahoo.com , indicando disponibilidade.
> Segue no final resumo do projeto.
> Alberto Davila
> amrdavila AT yahoo.com
> ***********
> GARSA: Genomic Annotation Resources for Sequence
> The growth of genome data and genome analysis
possibilities have 
> brought new levels of difficulty for scientists to
> integrate and deal with all this ever-coming
information. In this 
> scenario, we have conceived an environment, named
GARSA, aiming
> to facilitate the tasks of integrating and
presenting genomic 
> information from several Bioinformatics tools and
Genomic databases, 
> in a flexible way. GARSA is a user-friendly
web-based system designed 
> to analyze genomic data in the context of a
pipeline. It is an
> evolution of the ESTonSQL system (Lorenzini et al
2003), offering 
> enhanced functionalities like multiproject support,
improved database 
> schema, more analysis tools, user authentication
and a more user-
> friendly interface. GARSA works in Linux-based
systems using Perl, 
> Bioperl, CGI, Apache and MySQL. An installer has
been written using
> shell script. EST and GGS data can be analysed
using the system since 
> it accepts: a) chromatograms, b) download of
sequences from GenBank, 
> c) Fasta files stored locally or d) a combination
of all 3. GARSA 
> uses the phred/phrap package to process
chromatograms, evaluate 
> quality of traces and remove vector contamination.
Clustering is
> done using the CAP3 program. Contigs are submitted
to Blast analyses 
> with NR, NT, swiss-prot and any other database
choosen by the user. 
> Conserved domain searches are also performed using
the CDD tool of 
> NCBI and Interpro have been implemented in the
pipeline as well. Once 
> all the above similarity searches have been
performed, the user
> can select some contigs and results to perform
multiple alignment 
> using ClustalW and phylogeny analysis using Phylip.
A feature for 
> registered users to enter comments or annotations
on any contigs has 
> been added. The system is being used for the
analyses of
> GSS sequences of Trypanosoma vivax, and EST data
will be included 
> too. Other gene discovery projects will be included
in the system as 
> GARSA can deal now with multiple projects.

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