Frequently, homology is used as a reason to transfer knowledge about function or structure from known to unknown proteins. Although phylogenies are the method of choice when attempting to determine homology, the most frequently used marker is pairwise sequence similarity.
The problem of finding groups of co-regulated genes across a number of microarray experiments is quite similar to the problem of finding groups of homologous proteins in a...
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MacGDE for Mac OS 2.4
A set of programs for multiple sequence alignment and analysis. The programs use an expandable user interface which allows the addition of external analysis functions without any rewriting of code. The system supports several data types, nucleic and amino acid sequences, text, and masking sequence, and three forms of color highlighting. The system has several external analysis functions included for such things as automated alignment,...
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Platform: Mac, Linux , 10.4,or,later
Scoring and Ranking of Sequence-Structure Alignments. Quasar is used to score and rank sequence and structure alignments.With the growing gap between the number of known protein sequences in databases like SwissProt/TrEMBL and the number of experimentally determined protein structures in the PDB, automated structure prediction methods like homology modeling and fold recognition have become valuable tools for assigning potential folds to new...
Unrooted is a tree drawing software able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). Trees are drawn in an unrooted way, that is, using a circular shape, with labels aligned with terminal branches.Use of Unrooted:A file selection box allows to select the tree file which then is drawn on the screen. A postscript output of the drawing can be prepared (on Macintosh, the...
Create phylogenetic trees with this tool. NJplot is a tree drawing software able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially handy for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.Use of NJPlotAny rooting of the unrooted tree can be interactively specified using the mouse. NJplot...
WPDB Database Loader 2.0
The Protein Data Bank Through Microsoft Windows. Analyze 3D structure of biological macromolecules fast and easy. WPDB Database Loader help you interrogate the 3-dimensional structure of biological macromolecules as found in the Protein Data Bank (PDB) using query and display tools like those shown above.WPDB Database Loader Features:Scientific:1. Find structures based on text and sequences searches (mismatches allowed).2. Sequence alignment...
Fasta File Comparer 1.2.3913
Compares protein sequences from different Fasta files. FFasta File Comparer software will compare portions of the protein sequences in the source Fasta file with those in the comparison Fasta file and write the matching proteins and sequences to an output text file. The user must specify the length of residues to use when comparing the two protein files. The output file will contain the names of the proteins with residues in common, the actual...
TESD (Transposable Element Simulator Dynamics) 1.0
TESD (Transposable Element Simulator Dynamics) is a scientific software developed by the Laboratoire de Biom trie et Biologie Evolutive, it simulates the number of genomic TE copies in different populations across generations (according to the Island Model), using classical models of TE dynamics. The parameters of the models (transposition and excision rates, selection intensity, recombination rate, migration rate, population sizes and number...
MB DNA Analysis 6.84
MB is a FREE software for DNA analysis. MB stands for MolecularBiological DNA Analysis. MB is a free Windows DNA analysis program. On other systems (Linux, Macintosh) it is possible to emulate the program.MB is a relative small and easy-to-use program. It includes the most common features for the analysis of DNA and protein sequences. These are: restriction sites search, restriction mapping, amino protein analysis, multiple sequence alignment,...
PanOCT, Pan-genome Ortholog Clustering Tool, is a program written in PERL for pan-genomic analysis of closely related prokaryotic species or strains. Unlike traditional graph-based ortholog detection programs, it uses micro synteny or conserved gene neighborhood (CGN) in addition to homology to accurately place proteins into orthologous clusters.
Prospect Interface 1.04
Bio::Prospect:: is a Perl API to thePROSPECT threading application. The modules provide for programexecution, results parsing, multiple sequence alignments inferred frompairwise sequence-structure alignments, and rudimentary homology models.
t2prhd is a Perl script which generates simple diagrams that highlight relationships of sequence repeats detected by using a profile HMM in two sequences. Homology relations are identified on the basis of the phylogeny of repeats.