Expressed sequence tag annotation software tools | Transcription data analysis
Expressed sequence tags (EST) represent short, unedited, randomly selected single-pass sequence reads derived from cDNA libraries, providing a low-cost alternative (also called ‘poor’ man's genome) to whole genome sequencing and specifically relevant to the transcriptome of an organism at various stages of development or under different experimental conditions. The analysis of EST data can enable gene discovery, complement genome annotation, aid gene structure identification, establish the viability of alternative transcripts, guide single nucleotide polymorphism (SNP) characterization and facilitate proteomic exploration.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Analyses large Expressed Sequence Tags (EST) and mRNA databases in which the sequences are clustered based on pairwise sequence similarity. TGICL then assembles them by individual clusters (optionally with quality values) to produce longer, more complete consensus sequences. The system can run on multi-CPU architectures including SMP (Symmetric multiprocessing) and PVM (Parallel Virtual Machine).
A portable and easily configurable genome annotation pipeline. MAKER allows smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. It identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER's inputs are minimal and its ouputs can be directly loaded into a Generic Model Organism Database (GMOD). They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER is available for download and can be tested online via the MAKER Web Annotation Service (MWAS).
Meets the Expressed Sequence Tags (EST) annotation and data management requirements of multiple high-throughput EST sequencing projects. ESTIMA is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology (GO) associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow the user to query and retrieve information. Further, query results are interconnected among the various EST properties. Users may run their own EST processing pipeline, search against preferred reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline.
Translates expressed sequence tags (ESTs) to produce putative peptides. prot4EST is a polypeptide prediction pipeline that incorporates several freely available software. It consists of several steps: (1) identification of ribosomal RNA (rRNA) genes, (2) similarity search, (3) ESTScan prediction, (4) DECODER prediction and (5) longest open reading frame (ORF). This software is designed to be used as a stand-alone tool, or as an integral part of the PartiGene process.
Aligns and merges sequence fragments resulting from shotgun sequencing or gene transcripts (expressed sequence tag (EST)) fragments in order to reconstruct the original segment or gene. EGassembler provides an automated as well as a user-customized analysis tool for cleaning, repeat masking, vector trimming, organelle masking, clustering and assembling of ESTs and genomic fragments. The web server is publicly available and provides the community an all-in-one online application web service. Running on a Sun Fire 15K supercomputer, a significantly large volume of data can be processed in a short period of time. The results can be used to functionally annotate genes, to facilitate splice alignment analysis, to link the transcripts to genetic and physical maps, design microarray chips, to perform transcriptome analysis and to map to KEGG metabolic pathways.
Proposes a set of analytical procedures that automatically verify, cleanse, store and analyze ESTs (Expressed Sequence Tags) generated on high-throughput platforms. ESTAP uses a relational database to store sequence data and analysis results, which facilitates both the search for specific information and statistical analysis. ESTAP provides for easy viewing of the original and cleansed data, as well as the analysis results via a Web browser. It also allows the data owner to submit selected sequences to dbEST in a semi-automated fashion.