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Expressed sequence tag annotation software tools | Gene expression 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 (Adams et…
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EGassembler
Web

EGassembler

Aligns and merges sequence fragments resulting from shotgun sequencing or gene…

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…

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ESAP plus
Web

ESAP plus Expressed sequence tag Analysis Pipeline Plus

Helps to develop Simple Sequence Repeat (SSR) markers from a large Expressed…

Helps to develop Simple Sequence Repeat (SSR) markers from a large Expressed Sequence Tag (EST) collection. ESAP plus can handle large scale design of EST-SSR primers that is needed in most plant…

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TGICL
Desktop

TGICL TTIGR Gene Indices clustering tools

Analyses large Expressed Sequence Tags (EST) and mRNA databases in which the…

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…

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ESTprep
Desktop

ESTprep

Preprocesses expressed sequence tag (EST) sequences. ESTprep identifies the…

Preprocesses expressed sequence tag (EST) sequences. ESTprep identifies the location of features present in ESTs and allows the sequence to pass only if it meets various quality criteria. The…

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ESTAP
Web
Desktop

ESTAP EST Analysis Pipeline

Proposes a set of analytical procedures that automatically verify, cleanse,…

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…

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ESTAnnotator
Web

ESTAnnotator

Supports the search of functional annotations of novel transcript sequences…

Supports the search of functional annotations of novel transcript sequences through automatic analysis of EST sequences. ESTAnnotator, in a first quality check step repeats, masks vector parts and…

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PipeOnline
Web

PipeOnline

Analyses and transforms large collections of raw DNA-sequence data by calling…

Analyses and transforms large collections of raw DNA-sequence data by calling the quality of bases, screening and removing vector sequences, assembling and rewriting consensus sequences of redundant…

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ECLAT
Web

ECLAT

This is a server for the classification of ESTs from mixed EST pools (from…

This is a server for the classification of ESTs from mixed EST pools (from fungus infected plants). ECLAT is based on the machine learning algorithm Support Vector Machines and uses codon frequencies…

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JUICE
Desktop

JUICE

Enables the user to easily upload, organize, visualize and search the different…

Enables the user to easily upload, organize, visualize and search the different types of data generated in an expressed sequence tag (EST) project pipeline. JUICE is a data management system which…

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EST-PAC
Desktop

EST-PAC

Annotates expressed sequences tag (EST). EST-PAC is adapted for laboratories…

Annotates expressed sequences tag (EST). EST-PAC is adapted for laboratories with limited bioinformatics resources and expertise. It offers a solution to implement a database system for the…

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est2genome
Desktop

est2genome

Aligns EST sequences to genomic DNA sequence. est2genome aids the prediction of…

Aligns EST sequences to genomic DNA sequence. est2genome aids the prediction of genes by sequence homology. It aligns a set of spliced nucleotide sequences (ESTs cDNAs or mRNAs) to an unspliced…

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E2G
Web

E2G

Extends the volume of data that can be mapped in reasonable time, and makes…

Extends the volume of data that can be mapped in reasonable time, and makes this improved efficiency available as a web service. e2g is a web-based server which efficiently maps large expressed…

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ESTpass
Web

ESTpass

Processes and annotates sequence data from expressed sequence tag (EST)…

Processes and annotates sequence data from expressed sequence tag (EST) projects. ESTpass executes a back-end EST analysis pipeline consisting of three consecutive steps. The first is cleansing the…

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ESTExplorer
Web

ESTExplorer

Provides a comprehensive workflow system for expressed sequence tag (EST) data…

Provides a comprehensive workflow system for expressed sequence tag (EST) data management and analysis. ESTExplorer uses a distributed control approach in which the most appropriate bioinformatics…

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WebTraceMiner
Web

WebTraceMiner

Provides a public sequence processing service for raw expressed sequence tag…

Provides a public sequence processing service for raw expressed sequence tag (EST) traces. WebTraceMiner focuses on detection and mining of sequence features that help characterize 3′ and 5′…

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OREST
Web

OREST

Provides a web-based expressed sequence tag (EST) analysis pipeline for gene…

Provides a web-based expressed sequence tag (EST) analysis pipeline for gene assignment and systematic functional annotation of large amounts of DNA sequences. OREST allows mapping of user data to…

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EST-PAGE
Desktop

EST-PAGE

Provides a bioinformatics solution for expressed sequence tags (EST) data…

Provides a bioinformatics solution for expressed sequence tags (EST) data entry, database management, GenBank submission, process control and data retrieval from a unified web interface. EST-PAGE can…

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ESTweb
Web

ESTweb

Is designed for uniform data processing and storage for large-scale Expressed…

Is designed for uniform data processing and storage for large-scale Expressed Sequence Tag (EST) sequencing projects. ESTweb package provides for: (a) reception of sequencing chromatograms; (b)…

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ESTPiper
Web
Desktop

ESTPiper Expressed Sequence Tag Piper

Streamlines the typical process of Expressed Sequence Tag (EST) analysis.…

Streamlines the typical process of Expressed Sequence Tag (EST) analysis. ESTPiper web interface guides users through each step of base calling, data cleaning, assembly, genome alignment, annotation,…

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MediPlEx
Web

MediPlEx MEDIcago truncatula multiPLe EXpression analysis

Identifies genes activated in Medicago truncatula AM roots. MediPlEx combines…

Identifies genes activated in Medicago truncatula AM roots. MediPlEx combines the different kinds of gene expression datasets. It gathers information on the composition of the relevant Tentative…

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TransSeqAnnotat…
Web

TransSeqAnnotator

Provides a workflow for large-scale analysis of transcriptomic data with the…

Provides a workflow for large-scale analysis of transcriptomic data with the most appropriate bioinformatics tools for data management and analysis. TransSeqAnnotator automatically cleans, clusters,…

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ESTIMA
Web
Desktop

ESTIMA Expressed Sequence Tag Information Management and Annotation

Meets the Expressed Sequence Tags (EST) annotation and data management…

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…

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ParPEST
Web

ParPEST Parallel Processing of ESTs

Performs an exhaustive and reliable analysis on expressed sequence tags (EST)…

Performs an exhaustive and reliable analysis on expressed sequence tags (EST) data. ParPEST also provides a curated set of information based on a relational database. Moreover, it is designed to…

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