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AACompIdent	Internet Browser
Identify a protein by its amino acid composition.
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: Expasy
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: NCBI
BlockSearch	Unix
BlockSearch is a program developed for Digital's VAX and Alpha computer systems that utilizes the BLOCKS database for the functional analysis of new protein sequences. BlockSearch is fast and user-friendly, and the code is easily portable to other platforms.
	Download  (45 kb, 06-Dec-1993)
CIDentify 1.05 (MS-DOS)	MS-DOS
CIDentify is a homology-based database search algorithm designed to aid in the identification of unknown peptides by mass spectrometry (MS). It is designed to be used in conjuction with Lutefisk97.
	Download  (383 kb, 12-Oct-1998)
CIDentify 1.05 (Mac)	Mac
CIDentify is a homology-based database search algorithm designed to aid in the identification of unknown peptides by mass spectrometry (MS). It is designed to be used in conjuction with Lutefisk97.
	Download  (376 kb, 12-Oct-1998)
CIDentify 1.05 (Unix)	Unix
CIDentify is a homology-based database search algorithm designed to aid in the identification of unknown peptides by mass spectrometry (MS). It is designed to be used in conjuction with Lutefisk97.
	Download  (337 kb, 12-Oct-1998)
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: 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: CLC bio
CombSearch	Internet Browser
An experimental unified interface to query several protein identification tools accessible on the web.
Web Site: University of Geneva
Consense 1.1	MS-DOS
A program to calculate consensus sequences from alignments, which allows identification of protein domains and improvement of alignments.
	Download  (35 kb, 21-Jun-1993)
Expression	Windows
Expression is a revolutionary new application for DNA and protein sequence analysis. Utilising a novel interface, Expression makes complex computational analyses of sequence information incredibly simple. Expression uses the very latest computing technology to set new standards in the way sequences are analysed. Features include: Sequence Annotation,Graphical Sequence Map, Degenerate DNA and Amino Acid Sequence Support, Restriction Analysis, Primer Design and Analysis, ORF Prediction, Pattern Finding, Reverse Translation, GenBank Searching, Pattern and Motif Identification, Multiple Sequence Alignment, and Protein Structure Prediction.
Web Site: Genamics
FPAT	Internet Browser
Regular expression searches in protein databases.
Web Site: IBC, Washington University
Fasta3	Internet Browser
FASTA version similarity searching.
Web Site: EBI
Frame-ProfileScan	Internet Browser
Scans a short DNA sequence against protein profile databases (including PROSITE).
Web Site: ISREC
Gene and Protein Synonym DataBase (GPSDB)	Internet Browser
GPSDB (Gene and Protein Synonym DataBase) is the most comprehensive collection of gene and protein name synonyms, organized by species. Freely accessible on the web. Published by PharmaDM.
Web Site: BioMinT
International Journal of Biological & Medical Research (IJBMR)	Internet Browser  Linux  Windows
International Journal of Biological & Medical Research (IJBMR) publishes papers describing original research in all areas of contemporary biological and medical fields. Submitted original research papers should represent a novel and important contribution to the understanding of any area of biological and medical research and provide mechanistic insights into the process. All submitted articles should report original, previously unpublished research results, experimental or theoretical, and will be peer-reviewed. Articles submitted to the journal should meet these criteria and must not be under consideration for publication. Manuscripts should follow the style of the journal and are subject to both review and editing. International Journal of biological and medical research is an international peer-reviewed multidisciplinary online journal published in quarterly in the months of January, April, July and October. The journal accepts Original Articles, Review Articles, Case Report and Short Report. Scope of the Article All Biological & Medical Sciences like Anesthesiology, Animal Research, Basic medical sciences, Biochemistry, Biotechnology, Bioinformatics, Biophysics, Biology, Cancer biology, Cardiology, Cardio Thoracic Surgery, Dibetology, Dermatology, ENT, Endocrinology, Free radical Biology, General surgery, General Medicine, Genetics, Gastroenterology, Gynecology, Hematology, Herbal Therapy, Human physiology, Immunology, Infertility, Infectious Diseases, Laboratory Medicine & Techniques, Microbiology, Molecular Biology, Nanotechnology, Neonatology, Neurology, Nephrology, Nursing care, Nutrition, Oncology, Orthopedics, Ophthalmology, Pathology, Plant Study, Plant Bio Technology, Pharmacology, Pulmonology, Pediatrics, Psychiatry, Rheumatology, STDs, Stem Cell Research, Toxicology, Urology & Virology, etc
Web Site: BioMedSciDirect publications
International Journal of Biological and Medical Research (IJBMR)	Internet Browser  MS-DOS  Windows
International Journal of Biological & Medical Research (IJBMR) publishes papers describing original research in all areas of contemporary biological and medical fields. Submitted original research papers should represent a novel and important contribution to the understanding of any area of biological and medical research and provide mechanistic insights into the process. All submitted articles should report original, previously unpublished research results, experimental or theoretical, and will be peer-reviewed. Articles submitted to the journal should meet these criteria and must not be under consideration for publication. Manuscripts should follow the style of the journal and are subject to both review and editing. International Journal of biological and medical research is an international peer-reviewed multidisciplinary online journal published in quarterly in the months of January, April, July and October. The journal accepts Original Articles, Review Articles, Case Report and Short Report. Scope of the Article All Biological & Medical Sciences like Anesthesiology, Animal Research, Basic medical sciences, Biochemistry, Biotechnology, Bioinformatics, Biophysics, Biology, Cancer biology, Cardiology, Cardio Thoracic Surgery, Dibetology, Dermatology, ENT, Endocrinology, Free radical Biology, General surgery, General Medicine, Genetics, Gastroenterology, Gynecology, Hematology, Herbal Therapy, Human physiology, Immunology, Infertility, Infectious Diseases, Laboratory Medicine & Techniques, Microbiology, Molecular Biology, Nanotechnology, Neonatology, Neurology, Nephrology, Nursing care, Nutrition, Oncology, Orthopedics, Ophthalmology, Pathology, Plant Study, Plant Bio Technology, Pharmacology, Pulmonology, Pediatrics, Psychiatry, Rheumatology, STDs, Stem Cell Research, Toxicology, Urology & Virology, etc...
Web Site: BioMedSciDirect publications
Jouarnal of Qafqaz Universty
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
MOWSE	Internet Browser
Peptide mass search tool.
Web Site: Daresbury Laboratory
MPSA	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.
Web Site: Multiple Protein Sequence Analysis
Mascot	Internet Browser
Peptide mass fingerprint, sequence query and MS/MS ion search.
Web Site: Matrix Science Ltd., London
MedScan	Windows
MedScan is an automated desktop system based on advanced Natural Language Processing (NLP) technologies, extracting information about protein functions and pathways from MEDLINE abstracts. The accuracy of MedScan when applied to the whole PubMed was found to be 97% (less than 3% of false positives).
Web Site: Ariadne Genomics
MultiIdent	Internet Browser
Identify proteins with pI, Mw, amino acid compositon, sequence tag and peptide mass fingerprinting data.
Web Site: Expasy
PDBMotif 1.3	Unix
A tool for the automatic identification and display of motifs in protein structures. Requires C compiler.
	Download  (10 kb, 16-Jun-1995)

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