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AACompIdent Internet Browser
Identify a protein by its amino acid composition.
Web Site Home Web Site: Expasy

AACompSim Internet Browser
AACompSim is 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.
Web Site Home Web Site: Expasy

ABI to FASTA free converter Windows
This free tool will batch convert all (selected) ABI files to FASTA files. All you need to do is to locate your ABI chromatogram files and press the CONVERT button. With this automatic converter you can convert hundreds or thousands of ABI chromatogram files in seconds. All with A SINGLE PUSH OF A BUTTON! ---------- No installation process is required.
Web Site Home Web Site: DNA Baser Contig Assembler

AMAS: Analyze Multiple Alignments of Protein Sequences Unix
Allows the identification of functional residues by comparison of sub-groups of sequences arranged on a tree.
Web Site Home Web Site: The Barton Group

Aligner Internet Browser
With this tool you can align easily your multiple sequences DNA or protein, based on a Clustalw engine.
Web Site Home Web Site: JustBio.com

Antheprot 2.9 MS-DOS  Unix  Windows
This is a protein sequence analysis package.
Web Site Home Web Site: Institut de Biologie et Chimie des Proteines

BLAST 2.0 Internet Browser  MS-DOS
A tool used to identify any potential homologies of a given DNA or protein sequence with those stored in GenBank.
Web Site Home Web Site: NCBI

Bic_SW Internet Browser
Compugenīs Bic2īs Smith & Waterman algorithm implementation for protein database searches.
Web Site Home Web Site: EBI

BioMedCAChe Linux  Mac  Unix  Windows
BioMedCAChe is a new computer-aided chemistry software package designed specifically for bio- and medicinal chemists. It provides powerful software tools to accelerate the drug discovery process. BioMedCAChe enables to analyze protein sequences and optimize their 3D structures, build protein structures by homology, dock ligands, and model enzyme reactions using whole enzymes.
Web Site Home Web Site: BioMedCAChe - Software for bio and medicinal Chemists

BioToolKit Mac  Windows
BioToolKit is a collection of tools frequently used by bench biomedical scientists. Functions include centrifugation speed/force conversion, molecular weight calculation for chemicals, oligos, and peptides, molar concentration calculator, OD calculator, recipe calculator, clinical calculator, primer design, peptide antigen design, grade book, and label printing.
Web Site Home Web Site: Chang Bioscience

CAChe Linux  Mac  Unix  Windows
CAChe is a leading computer-aided chemistry modelling package designed for experimental chemists conducting research in life science, materials and chemical, as well as for undergraduate and graduate educators. CAChe lets every chemist visualize molecules in 3D, search for conformations, analyze chemical reactivity and predict properties of compounds with an easy-to-use, award-winning interface on desktop computers.
Web Site Home Web Site: Use CAChe to model your experiments

CELL Suite Windows
Incellico's Cell Suite being offered as a modular portfolio of research and discovery tools that will individually, and as a whole, respond to the specific challenges faced by life sciences researchers across the spectrum of biotechnology and bioinformatics problem solving. CELL acts as a librarian of public and private databases, automatically cross-referencing entities like genes and proteins that appear in those databases, and building a searchable, ontology-based network of cross-references that reveals the relationships between entities of interest to a user.
Web Site Home Web Site: Incellico

CLC Combined Workbench Linux  Mac  Windows
CLC Combined Workbench 1.0 aggregates all DNA sequence analyses of CLC Gene Workbench and all protein sequence analyses of CLC Protein Workbench. All analyses are fully integrated in one single, user-friendly, and intuitive software application. Some analyses are - Assembly of DNA sequencing data - Advanced primer design - Molecular cloning - Automatic SNP annotation of sequences - Secondary protein structure prediction - Signal Peptide Prediction (SignalP) - Transmembrane helix prediction (TMHMM) - Protein family analysis (PFAM) - 2 types of alignments - Phylogenetics - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Dot plots - Hydrophobicity analyses - Antigenicity analyses - Searches on GenBank, SwissProt, TrEMBL, and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

CLC Free Workbench 1.0 Linux  Mac  Windows
CLC Free Workbench creates a software environment enabling users to make basic bioinformatics analyses and smooth data management, combined with excellent graphical viewing and output options. Some bioinformatics features are: - GenBank searching and viewing (linear and circular views) - Multiple alignment of DNA, RNA and proteins (2 alignment algorithms) - Open reading frame determination - Translation from DNA to proteins (all genetic translation tables) - Reports with residue composition, molecular weight and iso electric point (for proteins) - Neighbor-joining and UPGMA phylogenies - Restriction site analysis and viewing - Other reporting facilities - Import/export to a number of data formats - Launch of external files - Detailed History Log
Web Site Home Web Site: CLC bio

CLC Gene Workbench Linux  Mac  Windows
CLC Gene Workbench 1.0 provides a wide range of advanced DNA sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. Some analyses are - Assembly of DNA sequencing data - Advanced primer design - Molecular cloning - Automatic SNP annotation of sequences - 2 types of alignments - Phylogenetics - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Dot plots - Hydrophobicity analyses - Searches on GenBank and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

CLC Protein Workbench Linux  Mac  Windows
CLC Protein Workbench 1.5 provides a wide range of advanced protein sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. Some analyses are - Advanced and integrated 3D molecular viewer - 2 types of alignments - Phylogenetics - Secondary protein structure prediction - Signal Peptide Prediction (SignalP) - Transmembrane helix prediction (TMHMM) - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Protein family analysis (PFAM) - Dot plots - Hydrophobicity analyses - Antigenicity analyses - Searches on GenBank, Swiss-Prot, TrEMBL, and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

ChloroP Internet Browser
The ChloroP WWW-server is able to predict: (1) whether or not an amino acid sequence contains an N-terminal chloroplast transit peptide, cTP and (2) the probable site for cleavage of the transit peptide (if it was predicted to exist in the first step).
Web Site Home Web Site: CBS

Cleaner Internet Browser
With this tool you can simply and quickly clean your sequences from unwanted text marks and spaces. This is useful after retrieving sequences from online databases for example.
Web Site Home Web Site: JustBio.com

Coils Internet Browser
Prediction of coiled coil regions in proteins (Lupas's method).
Web Site Home Web Site: EMB-net

Colorseq Internet Browser
Tool to highlight (in red) a selected set of residues in a protein sequence.
Web Site Home Web Site: PBIL

Compute pI/MW Internet Browser
Compute the theoretical pI and Mw from a SWISS-PROT or TrEMBL entry or for a user sequence.
Web Site Home Web Site: Expasy

DIG - Analysis, Reporting, Intelligence Linux  Unix  Windows
DIG is a Data Analysis, Reporting, Intelligence tool for data workers, labs, and webmasters. Use DIG to clean up duplicates, consolidate, trim, query, summarize large data set in Excel/Access, log files, Oracle, MySQL, lab or POS systems, or any databases. Comes with powerful Excel/Access add-ons, ad-hoc query & multi-dimensional analysis. Watch on-line demo, get a free 30-day trial, then pay $96/yr or $8/month.
Web Site Home Web Site: DigDB

DNATools Windows
DNATools has now been discontinued and replaced with SEQtools. SEQtools is a program 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.
Web Site Home Web Site: SEQtools

Delila Unix
This software is for information analysis of protein and nucleic-acid sequences.
Web Site Home Web Site: Schneider Lab

DiAlign Internet Browser  Linux  Unix
True multiple sequence alignment, not Needleman-Wunsch based. * No gap penalties (gaps are not introduced by the original alignment). * Alignment of whole segments and not of individual nucleotides or amino acids. * True multiple alignment, therefore independent of sequence order. * True multiple alignment of 200 sequences can be carried out on a workstation.
Web Site Home Web Site: Genomatix

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