Structural Biology Software Database
Structural Biology Software Database

Application Index

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Category: Gene and Protein Sequence Alignment, Phylogenetic Search and Analysis (25 entries)

Some software (e.g. CLUSTAL W, GCG) in this section is specific for doing the sequence alignment of proteins and DNA. Others(e.g. GCG, PHYLIP) are for searching for the evolutionary relationship between of gene (or protein) sequence from an organism and that from other organisms. Few such as "ConSurf" is for analysis of Functional Regions in Proteins using Phylogenetic Information.


3dSEARCH is a web-based program which does Protein Structure Alignment using the secondary structure superposition techniques.
View Application Entry for 3dSEARCH

AMAS (Analyse Multiply Aligned Sequences)

AMS allows you to run multiple sequence alignment via the Web. The program also can be obtained to run AMAS on your own Unix computer.
View Application Entry for AMAS (Analyse Multiply Aligned Sequences)

BVTech Plasmid

BVTech Plasmid is DNA sequence analysis and plasmid drawing software for Windows PCs.You can use it to plan your DNA cloning, draw high quality plasmid maps, analyse your DNA sequencing data, align sequences, and sequence format conversion. BVTech Plasmid is easy to use, powerful, and affordable for molecular biologists at any level.
View Application Entry for BVTech Plasmid


CLUSTAL W is a program for multiple sequence alignment which includes several modifications to improve results for the alignment of divergent protein sequences. It can be installe Unix or Windows or Power Macintosh or VMS machines.
View Application Entry for CLUSTAL W


ConSurf is an Algorithmic Tool for the Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information.
View Application Entry for ConSurf


DBGET is a simple database retrieval system for finding and obtaining specific entries of diverse databases.
View Application Entry for DBGET

FPS (Family Pairwise Search)

FPS is a web-based program which allows you to search a library of protein families with a protein sequence, GCG profile or BLAST checkpoint file that you provide. Your query will be analyzed at the San Diego Supercomputer Center using the Family Pairwise Search (FPS) algorithm, a method for scoring a biological sequence, GCG profile or BLAST checkpoint file against a family of sequences.
View Application Entry for FPS (Family Pairwise Search)

FSSP (Fold classification based on Structure-Structure alignment of Proteins)

The FSSP database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB). The classification and alignments are automatically maintained and continuously updated using the Dali search engine.
View Application Entry for FSSP (Fold classification based on Structure-Structure alignment of Proteins)


gBioSeq is a Biological sequence (ADN, protein) editor for GTK/Linux. It is in an early stage of development. The goal is to provide an easy to use software to edit DNA sequences under Linux (such as Seqapp on Macintosh).
View Application Entry for gBioSeq


gBioSeq is a Biological sequence (ADN, protein) editor for GTK/Linux. It is in an early stage of development. The goal is to provide an easy to use software to edit DNA sequences under Linux (such as Seqapp on Macintosh).
View Application Entry for gBioSeq


GBuilder is a Java application that is designed for the analysis and visualisation of collections and assemblies of sequences, e.g. from EST and high-throughput genomic sequencing. To access databases of sequence data and sequence analysis applications, GBuilder uses CORBA to connect to database servers located at the EBI.
View Application Entry for GBuilder

GCG (Genetics Computer Group)

GCG is a software package for the analyses of gene and protein sequences on unix machines. The GCG package for sequence analysis contains over 100 interrelated software programs. It enables scientists to analyze DNA and protein sequences by editing, mapping, comparing, and aligning them. This program is available for commercial uses.
View Application Entry for GCG (Genetics Computer Group)


GeneDoc is a Full Featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows.
View Application Entry for GeneDoc


InterPro is a useful resource for whole genome analysis and has already been used for the proteome analysis of a number of completely sequenced organisms.
View Application Entry for InterPro


Jpred is a internet web server that takes either a protein sequence or a mulitple alignment of protein sequences, and predicts secondary structure. It works by combining a number of modern, high quality prediction methods to form a consensus.
View Application Entry for Jpred


NNPREDICT is a web-based program that predicts the secondary structure type for each residue in an amino acid sequence.
View Application Entry for NNPREDICT

NW (pairwise Needleman and Wunsch sequence alignment program)

NW is an implementation of the Needleman and Wunsch dynamic programming sequence alignment algorithm. It reads PIR format sequence files and reports sequence similarity calculated in a number of different ways. Optionally it can generate a PIR format alignment file. NW is freely available for use by not-for-profit organisations. Commerical use is not permitted without the permission of the author. It is supplied as a gzipped tar file of source code.
View Application Entry for NW (pairwise Needleman and Wunsch sequence alignment program)


pDRAW lets you enter a DNA name and coordinates for genetic elements, such as genes, to be plotted on your DNA plots.
View Application Entry for pDRAW


PHYLIP is a package of programs for inferring phylogenies. It can be installed on Unix or Windows 95/98/NT or Power Macintosh machines.
View Application Entry for PHYLIP


PredictProtein is a web-based service for sequence analysis, and structure prediction. It can also be downloaded and installed on local machines.
View Application Entry for PredictProtein

Protein Colourer

Protein Colourer is a tool for colouring your amino acid sequences. The default settings will colour the sequence by the hydrophobicity of the amino acids. You can set the colouring scheme by changing the lists associated with each colour. Another scheme could be used to colour the amino acids by size.
View Application Entry for Protein Colourer


Sequery is a software which searches the sequences of the protein structures in the Protein Data Bank (PDB) for a particular pattern of residues, including exact matches, matrix calculated substitutions, and user-defined substitutions.
View Application Entry for Sequery


W2H is a WWW interface of the GCG Sequence Analysis Software Package.
View Application Entry for W2H


WIT is a www-based system to support the curation of function assignments made to genes and the development of metabolic models. It attempts to produce metabolic reconstructions for sequenced (or partially sequenced) genomes.
View Application Entry for WIT


YASS is a program to perform DNA local alignment (DNA similarity search) of sequences in fasta or plain format. Yass allows a highly-sensitive and fast search for similarity regions in DNA sequences. In comparative genomics projects, Yass is readily applied to chromosomal sequences of millions of base pairs.
View Application Entry for YASS

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