EST-PAC a web package for EST annotation and protein sequence prediction

Abstract

With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST) from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST) annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1) searching local or remote biological databases for sequence similarities using Blast services, 2) predicting protein coding sequence from EST data and, 3) annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics.

Lactation transcriptomics in the Australian marsupial, Macropus eugenii: transcript sequencing and quantification

“…In general, the Cap3 assembly resulted in tighter clustering and was therefore retained for further analysis. Sequence mapping and annotation were conducted using the EST-PAC platform incorporating ncbi BLAST suite, Estscan2 and HMMer software in a web oriented database system [ 44 ]. Estscan2 translation were used for the prediction of signal peptide by IPSORT [ 27 ] and SignalP [ 38 ].…”

A DNA transposon-based approach to functional screening in neural stem cells

“…14 (Griffiths-Jones et al, 2008) and similarity to novel putative pre-miRNAs was computed using Smith-Waterman algorithm as implemented in the fasta35 package (Pearson and Lipman, 1988). 454 sequencing reads from smallRNA libraries were downloaded from the Gene Expression Omnibus (Barrett et al, 2009) and aligned to putative pre-miRNAs using the blast-n program from the blastall package (Strahm et al, 2006) (-F F -p blastn -W 18 -S 1 -m 8). All data analysis was automated using the in-house developed miRNADiscovery pipeline.…”

Sma3s: A Three-Step Modular Annotator for Large Sequence Datasets

“… 12 Others are specialized for the annotation of specific sequence types, such as the EST-specific ESTAnnotator 13 and EST-PAC. 14 In addition, some tools are designed especially for the annotation of specific organisms. For example, BLANNANOTATOR assigns non-standard annotations to bacterial sequences.…”