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WildSilkbase: an EST database of wild silkmoths.

Arunkumar KP, Tomar A, Daimon T, Shimada T, Nagaraju J - BMC Genomics (2008)

Bottom Line: There are options to carry out searches for species, tissue and developmental stage specific ESTs in BLAST page.Other features of the WildSilkbase include cSNP discovery, GO viewer, homologue finder, SSR finder and links to all other related databases.We believe that WildSilkbase will be extremely useful for all those researchers working in the areas of comparative genomics, functional genomics and molecular evolution in general, and gene discovery, gene organization, transposable elements and genome variability of insect species in particular.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre of Excellence for Genetics and Genomics of Silkmoths, Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, ECIL road, Nacharam, Hyderabad-500 076, India. arun@cdfd.org.in

ABSTRACT

Background: Functional genomics has particular promise in silkworm biology for identifying genes involved in a variety of biological functions that include: synthesis and secretion of silk, sex determination pathways, insect-pathogen interactions, chorionogenesis, molecular clocks. Wild silkmoths have hardly been the subject of detailed scientific investigations, owing largely to non-availability of molecular and genetic data on these species. As a first step, in the present study we generated large scale expressed sequence tags (EST) in three economically important species of wild silkmoths. In order to make these resources available for the use of global scientific community, an EST database called 'WildSilkbase' was developed.

Description: WildSilkbase is a catalogue of ESTs generated from several tissues at different developmental stages of 3 economically important saturniid silkmoths, an Indian golden silkmoth, Antheraea assama, an Indian tropical tasar silkmoth, A. mylitta and eri silkmoth, Samia cynthia ricini. Currently the database is provided with 57,113 ESTs which are clustered and assembled into 4,019 contigs and 10,019 singletons. Data can be browsed and downloaded using a standard web browser. Users can search the database either by BLAST query, keywords or Gene Ontology query. There are options to carry out searches for species, tissue and developmental stage specific ESTs in BLAST page. Other features of the WildSilkbase include cSNP discovery, GO viewer, homologue finder, SSR finder and links to all other related databases. The WildSilkbase is freely available from http://www.cdfd.org.in/wildsilkbase/.

Conclusion: A total of 14,038 putative unigenes was identified in 3 species of wild silkmoths. These genes provide important resources to gain insight into the functional and evolutionary study of wild silkmoths. We believe that WildSilkbase will be extremely useful for all those researchers working in the areas of comparative genomics, functional genomics and molecular evolution in general, and gene discovery, gene organization, transposable elements and genome variability of insect species in particular.

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Related in: MedlinePlus

Web-shots of the database showing WildSilkbase query options, keyword search, homologue finder, SSR finder, GO viewer, BLAST search, cSNP data and download option.
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Related In: Results  -  Collection

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Figure 2: Web-shots of the database showing WildSilkbase query options, keyword search, homologue finder, SSR finder, GO viewer, BLAST search, cSNP data and download option.

Mentions: Database can be inspected via four different HTML pages to allow distinctive queries. The 'Search Options' page provides three different options namely, Keyword Search, Homolog Finder and SSR Finder, for searching the database. The 'Keyword Search' gives access to search the database by GO terms, EST clone ID and Unigene ID. 'Homolog Finder' allows end user to search for the homologue of the query sequence against 6 different insect species (Aedes aegypti, Anopheles gambiae, A. mellifera, B. mori, D. melanogaster and T. castaneum) based on BLAST search. 'SSR Finder' provides access to data on SSRs of wild silkmoth ESTs included in the database. Search results can be limited by the selection of SSRs of specific type belonging to a particular species. The output generated is displayed in a tabulated format (Figure 2).


WildSilkbase: an EST database of wild silkmoths.

Arunkumar KP, Tomar A, Daimon T, Shimada T, Nagaraju J - BMC Genomics (2008)

Web-shots of the database showing WildSilkbase query options, keyword search, homologue finder, SSR finder, GO viewer, BLAST search, cSNP data and download option.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483293&req=5

Figure 2: Web-shots of the database showing WildSilkbase query options, keyword search, homologue finder, SSR finder, GO viewer, BLAST search, cSNP data and download option.
Mentions: Database can be inspected via four different HTML pages to allow distinctive queries. The 'Search Options' page provides three different options namely, Keyword Search, Homolog Finder and SSR Finder, for searching the database. The 'Keyword Search' gives access to search the database by GO terms, EST clone ID and Unigene ID. 'Homolog Finder' allows end user to search for the homologue of the query sequence against 6 different insect species (Aedes aegypti, Anopheles gambiae, A. mellifera, B. mori, D. melanogaster and T. castaneum) based on BLAST search. 'SSR Finder' provides access to data on SSRs of wild silkmoth ESTs included in the database. Search results can be limited by the selection of SSRs of specific type belonging to a particular species. The output generated is displayed in a tabulated format (Figure 2).

Bottom Line: There are options to carry out searches for species, tissue and developmental stage specific ESTs in BLAST page.Other features of the WildSilkbase include cSNP discovery, GO viewer, homologue finder, SSR finder and links to all other related databases.We believe that WildSilkbase will be extremely useful for all those researchers working in the areas of comparative genomics, functional genomics and molecular evolution in general, and gene discovery, gene organization, transposable elements and genome variability of insect species in particular.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre of Excellence for Genetics and Genomics of Silkmoths, Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, ECIL road, Nacharam, Hyderabad-500 076, India. arun@cdfd.org.in

ABSTRACT

Background: Functional genomics has particular promise in silkworm biology for identifying genes involved in a variety of biological functions that include: synthesis and secretion of silk, sex determination pathways, insect-pathogen interactions, chorionogenesis, molecular clocks. Wild silkmoths have hardly been the subject of detailed scientific investigations, owing largely to non-availability of molecular and genetic data on these species. As a first step, in the present study we generated large scale expressed sequence tags (EST) in three economically important species of wild silkmoths. In order to make these resources available for the use of global scientific community, an EST database called 'WildSilkbase' was developed.

Description: WildSilkbase is a catalogue of ESTs generated from several tissues at different developmental stages of 3 economically important saturniid silkmoths, an Indian golden silkmoth, Antheraea assama, an Indian tropical tasar silkmoth, A. mylitta and eri silkmoth, Samia cynthia ricini. Currently the database is provided with 57,113 ESTs which are clustered and assembled into 4,019 contigs and 10,019 singletons. Data can be browsed and downloaded using a standard web browser. Users can search the database either by BLAST query, keywords or Gene Ontology query. There are options to carry out searches for species, tissue and developmental stage specific ESTs in BLAST page. Other features of the WildSilkbase include cSNP discovery, GO viewer, homologue finder, SSR finder and links to all other related databases. The WildSilkbase is freely available from http://www.cdfd.org.in/wildsilkbase/.

Conclusion: A total of 14,038 putative unigenes was identified in 3 species of wild silkmoths. These genes provide important resources to gain insight into the functional and evolutionary study of wild silkmoths. We believe that WildSilkbase will be extremely useful for all those researchers working in the areas of comparative genomics, functional genomics and molecular evolution in general, and gene discovery, gene organization, transposable elements and genome variability of insect species in particular.

Show MeSH
Related in: MedlinePlus