Comparisons & Alignments HOME Comparison & Alignments Functional Analysis Structural Analysis Other Analytical Tools
ALIGN A compendium of protein sequence alignments: it is a companion resource to PRINTS. For each fingerprint, there is a corresponding alignment in NBRF format, the root name of which is the relevant PRINTS code.
AllAll: Related Peptide Sequences Determines the relationship of each peptide sequence versus the others (all-against-all matching) and uses these results to construct and calculate phylogenetic trees, 2D optimal placements, multiple alignments, probabilistic ancestral sequences, variation indices and predictions of surface, interior and active site positions in the 3D fold.
BCM_Multiple Sequence Alignments A server for multiple sequence alignments.
Bioinformatics Links Directory Features curated links to molecular resources, tools and databases. All of the resources are well tested and are either free or available for a nominal fee. The links listed in this directory are selected on the basis of recommendations from bioinformatics experts in the field. All links contained in the NAR Webserver issue since 2003 are also listed.
BLAST 2 Sequences This tool produces the alignment of two given sequences using BLAST engine for local alignment. Currently only blastn and blastp programs are available.
BLASTula Identifies the function of newly discovered genes, characterize new sequences by performing extremely rapid comparisons against various large DNA and/or protein sequence databases.
Blocks WWW Server Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. Block Searcher, Get Blocks and Block Maker are aids to detection and verification of protein sequence homology. They compare a protein or DNA sequence to a database of protein blocks (current version), retrieve blocks, and create new blocks, respectively.
CLUSTALW A general purpose multiple alignment program for DNA or proteins.
DARWIN: Data Analysis and Retrieval With Indexed Nucleotide/Peptide Sequences An interactive tool for peptide and nucleotide sequence analysis. A growing library of functions for sequence management and analysis, statistics, numerics, graphics, parallel execution and more.
DCA: Divide-And-Conquer Multiple Sequence Alignment A program for producing fast, high quality simultaneous multiple sequence alignments of amino acid, RNA, or DNA sequences.
DIALIGN 2 An alignment program that relies on comparison of whole segments of the sequences instead of comparison of single residues. Pairwise as well as multiple alignments are constructed from gapfree pairs of equal length segments.
DIALIGN 2.1 A novel method for multiple alignment. DIALIGN constructs pairwise and multiple alignments by comparing whole segments of the sequences. No gap penalty is used. This approach is especially efficient where sequences are not globally related but share only local similarities, as is the case with genomic DNA and with many protein families.
EMBL_Dali A network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank.
EMBOSS "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.
EMBOSS Sequence Analysis Servers A suite of free software tools for sequence analysis, including that of GCG. There are a wide variety of programs that make up the suite, ranging in application from database searching to presentation of sequence data.
ESPript A program for analysis of protein sequences, multiple alignments, structural predictions, and more.
ExPASy_AACompSim Tool A tool which allows the comparison of the amino acid composition of a SWISS-PROT entry with all other SWISS-PROT entries so as to find the proteins whose amino acid compositions are closest to that of the selected entry.
ExPASy Proteomics Tools Provides tools from the ExPASy server as well as a few other servers.
gcg: genetics Computer Group It enables scientists to analyze DNA and protein sequences by editing, mapping, comparing, and aligning them. Other programs facilitate RNA secondary structure prediction, DNA fragment assembly, and evolutionary analysis. GCG serves molecular biologists by building practical tools that implement the important techniques of mathematical biology.
GENEDOC  A full featured multiple sequence alignment editor, analyzer and shading utility for windows.
GENQUEST  A sequence comparison program designed for rapid, sensitive comparison of DNA and protein sequences to DNA/protein databases.
HOVERGEN: Homologous Vertebrate Genes Database A database of homologous vertebrate genes, that allows to easily select sets of homologous genes among a given set of vertebrate species. HOVERGEN thus is particularly useful for: comparative sequence analysis, phylogeny, molecular evolution studies. More generally, HOVERGEN gives an overall view of what is known about a particular gene family.
JALVIEW A multiple alignment editor written entirely in java.
Jambw: Java-based Molecular Biology Workbench The programs and documentation have been put together in order to try to give a free access to the exploitment of the most common bioinformatics operations that a molecular biologist currently has.
JavaShade An interactive drawing program for preparing previously-generated multiple sequence alignments for publication, and for looking at the conservation of residues across the alignment.
LALIGN This is William Pearson's lalign program- find multiple matching subsegments in two sequences.
LALNVIEW A graphical program for visualizing local alignments between two sequences (protein or nucleic acids).
Match-Box Web Server  The Match-Box software proposes protein sequence alignment tools based on strict statistical criteria. The method circumvents the gap penalty requirement. The Match-Box program is particularly suitable for finding and aligning conserved structural motives, in particular in protein core.
Multiple Sequence Alignment For Proteins Ctree is a program to calculate multiple sequence alignments (MSA) of proteins with site specific estimates for the confidence of the alignment.
Pfam: Protein Families Database of Alignments and HMMs A large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. Pfam is a collection of protein families and domains. Pfam also contains multiple protein alignments and profile-HMMs of these families.
PropSearch PROPSEARCH was designed to find the putative protein family if querying a new sequence has failed using alignment methods. By neglecting the order of amino acid residues in a sequence, PROPSEARCH uses the amino acid composition instead. In addition, other properties like molecular weight, content of bulky residues, content of small residues, average hydrophobicity, average charge a.s.o. and the content of selected dipeptide groups is calculated from the sequence as well.144 such properties are weighted individually and are used as query vector.
RDP: Ribosomal Database Project II Provides ribosome related data services, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences.
RIFLE: Rapid Identification by Fragment Length Evaluation Compares restriction patterns of possibly unknown microorganisms against a database of theoretical restriction patterns generated from a 16S rDNA database. Restriction patterns of multiple restriction enzymes can be combined to improve the quality of identification, additional parameters allow the individual adaptation to laboratory processes.
ROSE: Random-model Of Sequence Evolution Rose implements a new probabilistic model of the evolution of RNA, DNA, or protein-like sequences. The data created by Rose are suitable for the evaluation of methods in multiple sequence alignment computation and the prediction of phylogenetic relationships.
SAM: Sequence Alignment and Modeling System The SAM software system is a collection of tools for creating and using linear hidden Markov models.
SEAVIEW A graphical multiple sequence alignment editor.
SIM: An Alignment Tool For Protein Sequences A program which finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence.
tmRDB Studies the structures and functions of the tmRNA The tmRDB provides aligned, annotated and phylogenetically ordered tmRNA sequences. The alignments of the sequences represent conserved secondary structure elements where each base pair is proven by comparative sequence analysis. Where possible, direct links to primary sources are established.
uRNA Database A tool to study the structures and functions of various uRNAs, providing aligned, annotated and phylogenetically ordered sequences. The alignments of the sequences represent conserved secondary structure elements where each base pair is proven by comparative sequence analysis. Where possible, there are direct links to GenBank via the accession number.
WWW SIGNAL SCAN Find and list homologies of published signal sequences with the input DNA sequence..

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