TranSeqAnnotator: large-scale analysis of transcriptomic data.

Ranjeeta Menon, Gagan Garg, Robin B. Gasser, Shoba Ranganathan

Research output: Contribution to journalConference paperResearchpeer-review

Abstract

The transcriptome of an organism can be studied with the analysis of expressed sequence tag (EST) data sets that offers a rapid and cost effective approach with several new and updated bioinformatics approaches and tools for assembly and annotation. The comprehensive analyses comprehend an organism along with the genome and proteome analysis. With the advent of large-scale sequencing projects and generation of sequence data at protein and cDNA levels, automated analysis pipeline is necessary to store, organize and annotate ESTs. TranSeqAnnotator is a workflow for large-scale analysis of transcriptomic data with the most appropriate bioinformatics tools for data management and analysis. The pipeline automatically cleans, clusters, assembles and generates consensus sequences, conceptually translates these into possible protein products and assigns putative function based on various DNA and protein similarity searches. Excretory/secretory (ES) proteins inferred from ESTs/short reads are also identified. The TranSeqAnnotator accepts FASTA format raw and quality ESTs along with protein and short read sequences and are analysed with user selected programs. After pre-processing and assembly, the dataset is annotated at the nucleotide, protein and ES protein levels. TranSeqAnnotator has been developed in a Linux cluster, to perform an exhaustive and reliable analysis and provide detailed annotation. TranSeqAnnotator outputs gene ontologies, protein functional identifications in terms of mapping to protein domains and metabolic pathways. The pipeline is applied to annotate large EST datasets to identify several novel and known genes with therapeutic experimental validations and could serve as potential targets for parasite intervention. TransSeqAnnotator is freely available for the scientific community at http://estexplorer.biolinfo.org/TranSeqAnnotator/.

LanguageEnglish
Article numberS24
Pages1-7
Number of pages7
JournalBMC Bioinformatics
Volume13
Issue numberSuppl 17
Publication statusPublished - 2012
EventAsia Pacific Bioinformatics Network (APBioNet) Eleventh International Conference on Bioinformatics (InCoB2012) - Bangkok, Thailand
Duration: 3 Oct 20125 Oct 2012

Fingerprint

Expressed Sequence Tags
Proteins
Protein
Pipelines
Computational Biology
Bioinformatics
Genes
Annotation
Gene Ontology
Workflow
Consensus Sequence
Similarity Search
Proteome
Metabolic Networks and Pathways
Experimental Validation
Transcriptome
Linux
Data Management
CDNA
Information management

Cite this

Menon, R., Garg, G., Gasser, R. B., & Ranganathan, S. (2012). TranSeqAnnotator: large-scale analysis of transcriptomic data. BMC Bioinformatics, 13(Suppl 17), 1-7. [S24].
Menon, Ranjeeta ; Garg, Gagan ; Gasser, Robin B. ; Ranganathan, Shoba. / TranSeqAnnotator : large-scale analysis of transcriptomic data. In: BMC Bioinformatics. 2012 ; Vol. 13, No. Suppl 17. pp. 1-7.
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abstract = "The transcriptome of an organism can be studied with the analysis of expressed sequence tag (EST) data sets that offers a rapid and cost effective approach with several new and updated bioinformatics approaches and tools for assembly and annotation. The comprehensive analyses comprehend an organism along with the genome and proteome analysis. With the advent of large-scale sequencing projects and generation of sequence data at protein and cDNA levels, automated analysis pipeline is necessary to store, organize and annotate ESTs. TranSeqAnnotator is a workflow for large-scale analysis of transcriptomic data with the most appropriate bioinformatics tools for data management and analysis. The pipeline automatically cleans, clusters, assembles and generates consensus sequences, conceptually translates these into possible protein products and assigns putative function based on various DNA and protein similarity searches. Excretory/secretory (ES) proteins inferred from ESTs/short reads are also identified. The TranSeqAnnotator accepts FASTA format raw and quality ESTs along with protein and short read sequences and are analysed with user selected programs. After pre-processing and assembly, the dataset is annotated at the nucleotide, protein and ES protein levels. TranSeqAnnotator has been developed in a Linux cluster, to perform an exhaustive and reliable analysis and provide detailed annotation. TranSeqAnnotator outputs gene ontologies, protein functional identifications in terms of mapping to protein domains and metabolic pathways. The pipeline is applied to annotate large EST datasets to identify several novel and known genes with therapeutic experimental validations and could serve as potential targets for parasite intervention. TransSeqAnnotator is freely available for the scientific community at http://estexplorer.biolinfo.org/TranSeqAnnotator/.",
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Menon, R, Garg, G, Gasser, RB & Ranganathan, S 2012, 'TranSeqAnnotator: large-scale analysis of transcriptomic data.', BMC Bioinformatics, vol. 13, no. Suppl 17, S24, pp. 1-7.

TranSeqAnnotator : large-scale analysis of transcriptomic data. / Menon, Ranjeeta; Garg, Gagan; Gasser, Robin B.; Ranganathan, Shoba.

In: BMC Bioinformatics, Vol. 13, No. Suppl 17, S24, 2012, p. 1-7.

Research output: Contribution to journalConference paperResearchpeer-review

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