| ISSC
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Unix VMS |
| ISSC are a set of programs for protein sequence comparison. ISSC calculates sensitive dot-plot comparisons for distantly related proteins sequences FILTER performs suboptimal alignments and recognition of reliably aligned regions in protein sequence comparisons. MALI performs mulitple sequence alignments. SCRUTINEER and OVERSEER perform pattern searching with flexible descriptors in amino acid and nucleotide databases. |
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Download (460 kb, 07-Oct-1992) |
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| Jouarnal of Qafqaz Universty
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| The Journal of Qafqaz University ` is a international refereed journal published twice a year since 1997 by Qafqaz University, Baku-Azerbaijan." "The Qafqaz University Journal accepts original unpublished articles and book reviews in the following fields: - social sciences, engineering, which includes computer engineering and industrial engineering..." Articles in English, Turkish and Azeri are available in full text. |
 Web Site: Journal of Qafqaz University
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| Jpred2
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Internet Browser |
| A consensus method for protein secondary structure prediction. |
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Web Site: EBI
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| KoriBlast
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Linux Mac Windows |
| KoriBlast is a reliable graphical environment dedicated to Blast data mining. KoriBlast proposes a graphical Blast scheduler capable of comparing at the same time multiple query sequences against multiple sequence databases using a network or a local Blast engine. KoriBlast provides several graphical user interfaces and analysis tools to view easily and to explore BLAST results in various ways, facilitating the interpretation of the data. Moreover, KoriBlast is capable of automatically retrieving data from NCBI Entrez databases, integrating valuable information directly in the graphical BLAST reports. Finally, all tha data available from KoriBlast can be queried allowing to quickly locate relevant information while reducing the amount of data to analyse. |
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Web Site: Korilog
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| MB DNA Analysis
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Windows |
| MB is a free multi-functional DNA/protein analysis program. It's main advantage is that it combines all of the most widely used features needed for an advanced molecular analysis of genomic/proteomic data. Features of MB include a fast restriction analysis algorithm (included plasmid / linear DNA drawing), promoter analysis, calculation of molecular weights and chemical properties of proteins, prediction of the secondary protein structures (after Chou-Fasman). Protein analysis also includes sequence translation and codon usage table calculation. Other features: hierarchical multiple sequence alignment tool (with a feature to compare secondary structure of proteins), phylogenetic tree building, dot plot, estimation of isoelectric point for proteins, primer design. A tool for the structural analysis of alpha helices is also included in the main package |
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Web Site: MB DNA Analysis
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| MBS ProtCalc
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Internet Browser |
| Calculate various protein parameters from your amino acid sequence, including pI, MW, and extinction coefficients. |
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Web Site: MBS
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| MDL-Pratt
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Unix |
| MDL-Pratt - Discovering Patterns and Subfamilies in Biosequences. MDL-Pratt is a perl script that calls Pratt (version 2.0) as a subprogram. |
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Download (4 kb, 01-Mar-1996) |
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| MDL-Pratt Documentation
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Unix |
| Documentation for MDL-Pratt. |
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Download (2 kb, 01-Mar-1996) |
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| MONSTER
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Internet Browser |
| MONSTER is a server for predicting the local structure and function properties of protein residues. MONSTER provides residue-wise annotation services, that include secondary structure, transmembrane-helix region, disorder region, protein-DNA binding site, \red {ligand-binding site}, local structure alphabet, solvent accessibility surface area, and residue-wise contact order prediction. MONSTER uses sequence-derived information (in the form of PSI-BLAST profiles), a window-based encoding scheme with an accurate kernel function to perform the classification or estimation. The user provides an amino acid sequence and selects the desired predictions, and submits a job to the MONSTER server. The results are emailed to the user as a link directing the user to a well formatted HTML output page |
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Web Site: Minnesota Residue Annotation Server
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| MPSA
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Linux Mac Unix Windows |
| MPSA is a stand-alone software package for protein sequence analysis with a high integrationlevel and Web client/server capabilities. It provides many methods and tools, which are integrated into an interactive graphical user interface. It is available for most Unix and non-Unix systems. MPSA is able to connect to a Web server (e.g. http://pbil.ibcp.fr/NPSA) in order to perform large-scale sequence comparison on up-to-date databanks. |
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Web Site: Multiple Protein Sequence Analysis
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| MPSRCH
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Linux Unix |
| The MPSRCH suite of sequence analysis tools is produced and developed by Edinburgh Biocomputing Systems (now Aneda Limited). It was originally developed 10 years ago to run on $1 million supercomputers but has now been re-engineered to run on reasonably priced, general purpose hardware. The software implements the full Smith-Waterman algorithm and is accessible free of charge at our company site. |
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Web Site: Aneda Limited
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| MW, pI, Titration curve
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Internet Browser |
| Also computes pI, composition and allows to see a titration curve. |
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Web Site: ABIM
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| MacP 1.2
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Mac |
| Protein property profile plots. |
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Download (190 kb, 25-Jun-1993) |
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| MacPattern 3.6
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Mac |
| MacPattern allows you to use the PROSITE and BLOCKS databases (or any other databases in the same format) for searching protein and nucleotide sequences for the occurrence of known patterns or similarities to protein blocks. |
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Download (473 kb, 01-Jun-1996) |
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| MacPattern 3.6 Information
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Mac |
| MacPattern allows you to use the PROSITE and BLOCKS databases (or any other databases in the same format) for searching protein and nucleotide sequences for the occurrence of known patterns or similarities to protein blocks. Information file only. |
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Download (9 kb, 01-Jun-1996) |
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| MacVector
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Mac |
| MacVector is an easy to use Macintosh application to help Molecular Biologists analyse, assemble and document DNA and protein sequences. MacVector, provides sequence editing, primer design, internet database searching, protein analysis, sequence alignment, phylogenetic reconstruction, coding region analysis, and a wide variety of other functions. The Assembler plugin provides contig assembly. Fully Leopard compatible. |
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Web Site: MacVector, inc.
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Download (456 kb, 02-Mar-1992) |
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| MitoProt 1.0.1
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Mac |
| MitoProt supplies a series of parameters that permit theoretical evaluation on mitochondrial targeting sequences and the importability. Finally, it provides the possibility to predict mitochondrial proteins harbouring targeting sequences. |
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Download (73 kb, 22-Jan-1996) |
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| MolBio++
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Unix |
| C++ class library for molecular biosequence analysis. |
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Download (540 kb, 11-May-1993) |
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| Motif
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MS-DOS |
| This program looks for a sequence motif defined by the user in the sequence(s) contained in the database file specified. |
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Download (35 kb, 08-Nov-1989) |
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| Multident
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Internet Browser |
| MultiIdent is a tool that allows the identification of proteins using pI, MW, amino acid composition, sequence tag and peptide mass fingerprinting data. One or more species and a SWISS-PROT keyword can also be specified for the search. |
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Web Site: Expasy
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| NetOGlyc
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Internet Browser |
| The NetOglyc WWW server produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins. |
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Web Site: CBS
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| NetOglyc: Type O-glycosylation
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Internet Browser |
| The NetOglyc WWW server produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins. |
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Web Site: CBS, Technical University of Denmark
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| NetPicoRNA
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Internet Browser |
| The NetPicoRNA World Wide Web server produces neural network predictions of cleavage sites of picornaviral proteases. |
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Web Site: CBS
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| Nrl-3d Database
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Internet Browser |
| NRL-3D is a sequence-structure database, which allows searches of PDB-derived data. |
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Web Site: Biomolecular Structure and Modelling Unit, University College London
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| O-GlycBase
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Internet Browser |
| O-GLYCBASE is a database of O-glycosylated glycoproteins. There are 180 present in the database. |
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Web Site: CBS, Technical University of Denmark
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