EGassembler

EGassembler processes, clusters, and assembles sequence fragments from expressed sequence tags (ESTs) and shotgun sequencing to produce assembled sequences for downstream functional annotation, transcript mapping, splice analysis, microarray probe design, and pathway mapping.

Key Features:

• Automated and customizable analysis: Provides configurable pipeline modes for automated or user-tailored processing of sequence datasets.
• Sequence preprocessing: Performs cleaning, repeat masking, vector trimming, and organelle masking to prepare high-quality input sequences.
• Clustering and assembly: Clusters ESTs and genomic fragments and assembles them into contigs for downstream analyses.

Scientific Applications:

• Functional annotation of genes: Uses assembled sequences to support gene function inference and annotation.
• Splice alignment analysis: Enables analysis of splicing patterns and alternative splicing events from assembled transcripts.
• Mapping transcripts: Facilitates linking transcripts to genetic and physical maps.
• Microarray chip design: Provides assembled sequences usable as probes for microarray design.
• Transcriptome analysis: Supports broad transcriptome analyses involving EST-derived assemblies.
• KEGG pathway mapping: Assists in mapping assembled sequences to KEGG metabolic pathways.

Methodology:

Performs sequence cleaning, repeat masking, vector trimming, organelle masking, clustering, and assembly of ESTs and genomic fragments.