| ProAnalyst 1.02
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MS-DOS |
| PROANALYST is an easy-to-use MS-DOS application to assist in the analysis of multiple protein alignments, studying the structure-function and structure-activity relationships in protein/peptide families. |
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Download (542 kb, 30-Aug-1996) |
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| ProMSED2
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Windows |
| ProMSED2 (Protein Multiple Sequence EDitor-2), Windows application for both automatic and manual DNA and protein sequence alignment, editing, comparison and analysis. |
 Web Site: BioInformer
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Download (461 kb, 06-Feb-1997) |
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| ProbeQuest Assistant
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Windows |
| ProbeQuest Assistant creates the following files for a probe/primer design: (1) List of exon-exon junction sites. (2) List of specified regions such as CDS. (3) List of restriction enzyme recognition sites. (4) Sequence file of genomes. (5) Sequence file of RNA regions in genome. (6) Multiple alignment file with position data. |
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Web Site: DYNACOM Co., Ltd.
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| ProfileWeight and ProPlot
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Unix |
| This package consists of two programs PROFILEWEIGHT and PROPLOT. PROFILEWEIGHT is a program to produce an alignment profile for use by the GCG program package. PROPLOT is a program for displaying dot-plots of (i) sequence versus sequence, (ii) sequence versus profile, and (iii) profile versus profile. |
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Download (200 kb, 20-Sep-1993) |
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| Protein Science Data Files
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MS-DOS Mac Unix VMS |
| Data files for evaluating sequence comparison programs as used in the paper, "Comparison of methods for searching protein sequence databases" (1995) Prot. Sci. 4:1145-1160. |
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Download (65 kb, 24-Dec-1995) |
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| RNA Baser - rRNA sequence assembly and analysis
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Mac Windows |
| RNA Baser represents an extension of DNA Baser, specialized in processing rRNA sequences. It is optimized for early integration of sequence and metadata. This way, the metadata will stay attached to the primary sequence information throughout the complete workflow of sequence analysis, until final submission. * * * * * * * * * * * * * * * * * * * * * * * RNA Baser it is optimized for data exchange with standard non-commercial software used for rRNA sequence analysis and submission. This is a joint project of HeracleSoftware, Ribocon GmbH and Max Planck Institute for Marine Microbiology in Bremen, Germany |
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Web Site: RNA Baser - sequence assembly and analysis
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| Redasoft
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Internet Browser Windows |
| Redasoft offers exciting new software tools designed to help you create and publish high quality genetic maps and perform sequence analysis quickly and easily. |
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Web Site: Redasoft
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| Restriction Map Alignment
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Unix |
| This program reads restriction maps and deciphers alignments using a quantic map alignment algorithm. |
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Web Site: USC Computational Biology
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| SAGA 0.9
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Unix |
| Sequence Alignment by Genetic Algorithm. SAGA is a multiple alignment program using a GA to minimise the Objective Functionnown as Weighted Sums of Pairs with affine or semi affine gap penalties. |
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Download (1514 kb, 27-Apr-1996) |
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| SAM-T99
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Internet Browser Linux Unix |
| SAM-T99 is a perl script using the SAM suite of tools for hidden Markov models to search for and align homologs of protein sequences. The web site uses the resulting alignment to do protein structure prediction(both fold recognition and secondary-structure prediction). |
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Web Site: HMM-based sequence query, Target99
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| SAM: Sequence Alignment and Modeling System
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Linux Unix |
| A hidden Markov modeling suite software system.Version 3.0 now includes the SAM-T99 script forfinding and aligning remote homologs of proteins.(Free to academics and non-profits) |
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Web Site: Baskin School of Engineering, UC Santa Cruz
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| SC rate
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Unix |
| A Perl5 program that evaluates the accuracy of protein sequence alignment with very low sequence identity. |
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Web Site: Medical Research Council
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| SEQAID 3.81
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MS-DOS |
| DNA and protein sequence analysis package. |
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Download (215 kb, 01-Aug-1991) |
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| SEQtools
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Windows |
| Program package for handling and analysis of nucleotide and protein sequences. In addition to many trivial functions, SEQtools includes advanced facilities for automated blast searching, sequence retrieval and design and layout of microarrays. |
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Web Site: SEQtools
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| SIM
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Internet Browser |
| Finds a user-defined number of best non-intersecting alignments between two protein sequences. Pairwise alignments can be viewed graphically. |
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Web Site: Expasy
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| SIM (MS-DOS)
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MS-DOS |
| The SIM program finds 'k' best non-intersecting alignments between two sequences or within one sequence. Using dynamic programming techniques, SIM is guaranteed to find optimal alignments. |
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Download (20 kb, 12-Feb-1991) |
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| SIM (Unix)
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Unix |
| The SIM program finds 'k' best non-intersecting alignments between two sequences or within one sequence. Using dynamic programming techniques, SIM is guaranteed to find optimal alignments. |
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Download (17 kb, 05-May-1992) |
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| SSS align
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Unix |
| A software implementation of the Smith/Waterman best local similarity algorithm which, in addition to the traditional Dayhoff PAM scoring scheme, has the ability to use secondary structure prediction in order to align sequences which have identities as low as 15% and still identify those sequences as significant. |
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Web Site: University of Edinburgh
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| STAMP
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Unix |
| A suite of programs for the comparison and alignment of protein three dimensional structures. The suite will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position. |
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Web Site: The Barton Group
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| STRAP
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Internet Browser Linux Mac Unix Windows |
| The free computer program STRAP aligns proteins by sequence and 3D-structure. It supports the simultaneous analysis of hundreds of proteins and integrates amino acid sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence and residue annotation. Protein files can easily loaded with Drag-and-Drop. The computed alignments can be exported as MS-Word, PDF, PS and raw text. Sequence features like glycosylated ore phosphorylated amino acids and active site residues are highlighted on the sequence. STRAP takes advantage of the 3D-viewer Pymol which is tightly integrated. Currently 80 Bioinformatics algorithms from authors from all over the world are embedded. These include structure prediction, sequence alignment, 3D-superposition, 3D-visualization, Blast and phylogenetic analysis. |
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Web Site: STRAP - A workbench for Protein Sequences and Structures
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| ScanPS (Unix)
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Unix |
| A local alignment method to search protein sequence databases with a query sequence or multiple alignment, and also allows all pairwise comparisons to be made between a set of sequences and can estimate the statistical significance of the alignments. |
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Web Site: The Barton Group
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| SeaView
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Unix |
| This is a multiple sequence alignment editor. |
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Web Site: Laboratoire de biometrie, genetique et biologie des populations
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| SeqAlign
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Unix VMS |
| SEQALIGN is a demonstration program which uses a modified Myers and Miller algorithm. The program introduces position-specific gap penalties into the existing algorithm. Thus, residue-dependent information such as structural preferences and existing gaps in the sequences can be applied to the alignment program. |
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Download (65 kb, 17-Sep-1994) |
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| SeqLogo
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Mac |
| Displaying consensus sequences by means of 'logos'. |
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Download (500 kb, 04-Feb-1991) |
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| SeqPup
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Mac Windows |
| A biosequence sequence editor and analysis program for multiple sequence alignments and single sequence editing. |
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Web Site: Indiana University
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