Package:

Description:

Ref:

eMOTIF

Create, scan, and search using discrete sequence motifs.

eBAS

eMOTIF Batch Analysis Suite. Permits eMOTIF licensees to analyze groups of proteins or entire proteomes for the presence of eMOTIFs in batch fashion.

3motif

Visualize discrete protein sequence motifs and their properties in 3 dimensions.

3matrix

Visualize probabilistic protein sequence motifs and their properties in 3 dimensions.

eMATRIX

Create, scan, and search using probabilistic sequence motifs.

LOCK 2

Performs vector-based protein structure alignment.

FoldMiner

Performs structural similarity searches and rapid, unsupervised structural motif discovery. Motifs are used to improve the sensitivity and specificity of the search.

CBA

Builds multiple structure alignments from pairwise superpositions using consistency as a driving force.

BioProspector

Discovers conserved transcription factor binding sites among upstream sequences from co-regulated genes. (more...)

MDScan

Discovers conserved transcription factor binding sites among upstream sequences from CHromatin Immune Precipitation experiments (CHIP) (more...)

eSIGNAL

Database of Medline MeSh terms and protein motifs that describe and detect signal transduction proteins.

ALION

Aligns two protein sequences using Needleman-Wunsch global alignment or Smith-Waterman local alignment (more...)

eConceptBuilder

A script for generating motifs from protein families defined by specific MeSh terms.

eProteome

A database of all significant eMOTIF patterns, eMATRIX patterns and BLAST similarities in open reading frames of 75 sequenced genomes.

eBLOCKS

A database of conserved, ungapped sequence alignments derived from SwissProt protein families using PSI-BLAST.

Alphabet

This program takes a database of aligned protein sequences in BLOCKS+ format and examines the alignments column-wise looking for groups of amino acids that co-occur in columns more frequently than expected. (more...)

SUBOPT

Aligns two protein sequences and can enumerate and display both optimal alignments and near optimal alignments within any distance delta of the optimal score.