bioinformatics platforms: from garsa to protozoadb the biowebdb consortium – garsa stingray...
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Bioinformatics platforms:from GARSA to
ProtozoaDB
The BiowebDB Consortium – http://www.biowebdb.org
GARSA STINGRAY ProtozoaDB ?
Alberto davila
e-mail: davila@fiocruz.br
G. A. R. S. A.Genomic Analyses Resources
for Sequence Annotation
http://garsa.biowebdb.orgEmail: davila@fiocruz.br
The BiowebDB Consortium – http://www.biowebdb.org
GARSA (2.0) features (short version)
i) User-based authentication and permissionsii) Trace analyses and triming
iii) Clusteringiv) Similarity analyses (nucleotide, protein and domain analyses)
v) Gene findersvi) Codon usagevii) CG content
viii) Distant homology detectionix) Phylogeny
x) Gene Ontology-based annotation
The BiowebDB Consortium – http://www.biowebdb.org
The BiowebDB Consortium – http://www.biowebdb.org
GARSAGARZAGARÇAHERON
Wikipedia: “... The herons are wading birds in the Ardeidae family. Some are named as egrets or bitterns. ... In February
2005 the Canadian scientist Dr Louis Lefebvre announceda method of measuring avian IQ in terms of their innovation infeeding habits. Herons were named among the most intelligent
birds based on this scale”.
http://en.wikipedia.org/wiki/Heron
The BiowebDB Consortium – http://www.biowebdb.org
Why GARSA needed to be developed ?
i) Need for integrated and user-friendly interfaces for annotationii) Need for a web-based annotation workflow
iii) Need for an annotation system able to deal with GSS, EST and ORESTES
iv) Need for a web-based collaborative system with user-based authentication
The BiowebDB Consortium – http://www.biowebdb.org
GARSA (2.0) features (short version)
i) User-based authentication and permissionsii) Trace analyses and triming
iii) Clusteringiv) Similarity analyses (nucleotide, protein and domain analyses)
v) Gene findersvi) Codon usagevii) CG content
viii) Distant homology detectionix) Phylogeny
x) Gene Ontology-based annotation
The BiowebDB Consortium – http://www.biowebdb.org
Software Function Version Reference
Phred Trace quality 0.020425.c
Ewing et al., 1998b
Cross match Remoção de seqüências de vetores0.020425
.cEwing et al., 1998a
CAP3 Clustering 3.0 Huang & Madan, 1999
Glimmer3* Gene prediction 3.0 Delcher et al., 1998
YACOP* Gene prediction 2.0 Tech & Merkl, 2003
Critica* + Gene prediction 1.05 Badger et al., 1999
RBS Finder*+ Ribosomal binding site 1.0 Susek et al., 2001
Zcurve*+ Gene prediction 1.02 Guo et al., 2003
BLAST Similarity 2.1.12 Altschul et al. 1997
RpsBlastConserved Domain Similarity
2.1.12 Altschul et al. 1997
Wu-Blast*+ Similarity 2.0 Lopez et al., 2003
Interpro Protein and domain similarity 3.3 Mulder et al., 2005
HMMER* Disntant homology detection 2.3.2 Eddy, 1998
geecee* G+C content 2.9.0.6 Rice, et al., 2000
cusp* Codon Usage 2.9.0.6 Rice, et al., 2000
tRNA-Scan* tRNA finder 1.23 Lowe et al., 1997
Clustalw* Multiple alignment 1.83 Thompson, et al. 1994
Muscle* Multiple alignment 3.52 Edgar et al., 2004
Probcons* Multiple alignment 1.10 Do et al., 2005
WebLogo* Logo Alignment visualization 2.8 Croocks et al. 2004
Phylip* Phylogeny 3.61 Felsenstein, 2005
Bioinformatics softwares implemented in the GARSA workflow
The BiowebDB Consortium – http://www.biowebdb.org
Privilege Permissions
admin This user is the project administrator and has write access to *all* data of a given project.
write Permission to execute some softwares of the worflow, phylogeny and psiblast, further than annotation of results.
read Permission to see *all* analyses results, search the database, execute the “comparative queries” and has *no* premission to modify or delete any data.
guest Restrictive permission. Only final results (no details) can be seen.
stat Very restrictive permission. Only overall statistics of the project can be seen. Editing or visualization of any other data is not allowed.
The BiowebDB Consortium – http://www.biowebdb.org
The BiowebDB Consortium – http://www.biowebdb.org
Administrative database (seqonsql) used by GARSA
The BiowebDB Consortium – http://www.biowebdb.org
The BiowebDB Consortium – http://www.biowebdb.org
The BiowebDB Consortium – http://www.biowebdb.org
The BiowebDB Consortium – http://www.biowebdb.org
The BiowebDB Consortium – http://www.biowebdb.org
The BiowebDB Consortium – http://www.biowebdb.org
The BiowebDB Consortium – http://www.biowebdb.org
STINGRAY
Introduction
The BiowebDB Consortium – http://www.biowebdb.org
STINGRAY uses as many Blast databases as available HardDisk space. The New Blast DB option is used to upload and format databases. TblastX, BlastX and BlastN
flavours are active by default. However, only 2 Blast runs are allowed to happen at the same time, in order to avoid CPU overload. E-value is configurable at this stage.
A figure showing best Blast results according to each frame is showed aiming to help with the identification of the right frame of CDS:
The BiowebDB Consortium – http://www.biowebdb.org
The BiowebDB Consortium – http://www.biowebdb.org
The “heroic” programmers
Daniel LorenziniPablo MendesLinair Campos Camila MazzoniGlauber WagnerThiago Satake
The PIs
Alberto DávilaMaria Luiza M. Campos
“Yoko” CavalcantiMarta Mattoso
Edmundo Grisard
ProtozoaDB
www.gusdb.org
The BiowebDB Consortium – http://www.biowebdb.org
ProtozoaDB architecture
http://protozoadb.biowebdb.org
If you don’t have too much time to spare because wantto be really competitive in science then use Really Simple
Syndication (RSS) and other Web2.0 technologies
The BiowebDB Consortium – http://www.biowebdb.org
(figure source: http://macmagazine.com.br/
Web2.0
Web 1.0 Web 2.0DoubleClick --> Google AdSense
Ofoto --> FlickrAkamai --> BitTorrent
mp3.com --> NapsterBritannica Online --> Wikipediapersonal websites --> blogging
evite --> upcoming.org and EVDBdomain name speculation --> search engine optimization
page views --> cost per clickscreen scraping --> web services
publishing --> participationcontent management systems --> wikis
directories (taxonomy) --> tagging ("folksonomy")stickiness --> syndication
The BiowebDB Consortium – http://www.biowebdb.org
Source: http://www.oreillynet.com/pub/a/oreilly/tim/news/2005/09/30/what-is-web-20.html
The BiowebDB Consortium – http://www.biowebdb.org
Source: http://pubcrawler.gen.tcd.ie/
The BiowebDB Consortium – http://www.biowebdb.org
iGoogle: http://www.google.com/ig
Journal’ feeds
The BiowebDB Consortium – http://www.biowebdb.org
Webservices
The BiowebDB Consortium – http://www.biowebdb.org
Source: http://www.ebi.ac.uk/Tools/webservices/
The BiowebDB Consortium – http://www.biowebdb.org
http://www.eu-eela.eu/
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