deepBase | Tool name | deepBase |
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| URL | http://deepbase.sysu.edu.cn/ |
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| Important features | A web-based resource to analyze deep sequencing data. |
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| Citations | Yang JH, Shao P, Zhou H, Chen YQ, Qu LH. deepBase: a database for deeply
annotating and mining deep sequencing data. Nucleic Acids Res. 2010
Jan;38(Database issue):D123-30. Epub 2009 Dec 4. PubMed PMID: 19966272; PubMed
Central PMCID: PMC2808990.
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| Year of publication | 2010 |
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| Rank by usage frequency | 100 |
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| Comments | |
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| Function | EXPERIMENTAL data analysis, http://deepbase.sysu.edu.cn/, A web-based resource to analyze deep sequencing data., Yang JH- Shao P- Zhou H- Chen YQ- Qu LH. deepBase: a database for deeply
annotating and mining deep sequencing data. Nucleic Acids Res. 2010
Jan;38(Database issue):D123-30. Epub 2009 Dec 4. PubMed PMID: 19966272; PubMed
Central PMCID: PMC2808990.
, 2010, 100, Online/ downloadable , I. SPECIES SUPPORTED INCLUDE: human- mouse- chicken- C. intestinalis- D. Melanogaster- C. elegans- Arabidopsis II. QUERY OR INPUT DATA: 1. Browser: select clade- genome- database- genomic position- ncRNA(miRNA- snoRNA- tRNA- rRNA- snRNA- scRNA- Mt_tRNA- misc RNA)- small RNA- RasRNA- cluster- heatmap- prediction(mirDeep) 2. Search: enter read sequence or read number- organism- chromosome location- and desired query (ncRNA name etc) as mentioned in (1). 3. BLAST: Input or upload sequence in FASTA format III. OUTPUT DATA: depending on the type of analysis chosen the results are depicted in tabular format- genome browser- library view browser and nas view graphic browser. Results may comprise of details on microRNA- snoRNA- tRNA- snRNA- scRNA- small RNA- Ras RNA- chromosome location- strand- read number- miRDeep predictions- miRDeep score etc. |
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