Biology: Bioinformatics: Online Services: Page 2

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CATEGORIES:

Ecological Databases (0)

Gene Expression and Regulation (6)

Genome Databases (7)

Homology Detection (11)

Molecular Biology Tools (3)

Phylogenetic Analysis (8)

Protein Analysis (22)

LINKS:

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Online Lab Reporting
http://www.labreporting.com/
A service that allows clinical laboratories to send test results to referring physicians over the internet. A help forum and FAQ pages are included.

PEDANT
http://pedant.gsf.de/
Completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes

PIR-International Protein Sequence Database
http://pir.georgetown.edu
produces a comprehensive, non-redundant, and expertly annotated protein sequence database. PIR features integrated annotation search to support functional/structural genomics and proteomic research.

Protein Structure Prediction Using Web Resources
http://cgat.ukm.my/spores/
SPORes is a website for protein structure prediction using the web browser as an interface to software that runs of web servers or other resources available over the world wide web.

ProteinLounge
http://www.proteinlounge.com
Bioinformatics portal which integrates protein information and many databases and research tools useful for researchers and students. Subscription based service.

ReadSeq
http://bimas.dcrt.nih.gov/molbio/readseq/
Convert various aminoacid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others.

SA National Bioinformatics Institute
http://www.sanbi.ac.za/
SANBI aims to bring genome information, computational biology, and analytical tools to the South African research community. Hosts SA National EMBNet Node, provides links to Sequence Retrieval System (SRS), GeneKraal, and TB Genomes Analysis Server. Research in Sequence Tag Alignment and Consensus Knowledgebase (STACK). Databases include BLAST search in Mycobacterium genome.

Scansite
http://scansite.mit.edu/
Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.

Searching GenBank
http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html
Text and similarity searching, provided by the National Center for Biotechnology Information (NCBI).

Sequence Analysis (Bielefeld University Bioinformatics Server)
http://bibiserv.techfak.uni-bielefeld.de/intro/seqdept.html
Collection of sequence analysis tools.

The XEMBL Project
http://www.ebi.ac.uk/xembl/
XEMBL provides access to the EMBL/GenBank/DDBJ Nucleotide Sequence Database, providing output in various XML standards.

Transcription Element Search Software (TESS)
http://www.cbil.upenn.edu/tess/
Very helpful software for locating and displaying transcription factor binding sites within DNA sequences - from the Univ. of Penn.

TRANSFAC-The Transcription Factor Database
http://www.gene-regulation.com/pub/databases.html#transfac
Very thorough compilation of transcriptional regulatory protein factors & their cognate gene promoter elements along with DNA sequence search & analysis programs - from GBF, Braunschweig, Germany.

Transterm - a database of mRNA regions and motifs
http://uther.otago.ac.nz/Transterm.html
Transterm - an interactive database of mRNA regions and motifs from all species and genomes. Users can browse the pre-computed data tables, search the sequence databases or search their own sequences.

Verbumculus Genetic Sequence Analyzer
http://www.cs.ucr.edu/~stelo/Verbumculus/
An interesting tool to discover and visualize over- or under-represented words in genetic sequences. Requires Java support in browser. Also available as a downloadable program.

Virtual Genome Center
http://alces.med.umn.edu/VGC.html
Online computational resources for PCR primer selection, similarity searching- from the Univ. of Minnesota.

Web Services at Institute of Microbial Technology, Chandigarh, India
http://imtech.res.in/raghava/www.html
Protein structure prediction (Protein Structural Classes, Secondary Structure Prediction), immunological methods (ProPred), genomics & proteomics (Genome Wise Sequence Similarity Search, Spectral Repeat Finder, 2D Gel Comparison, protein coding gene by Fast Fourier Transform), and biological databases.

YMF - DNA Motif Finding Program
http://abstract.cs.washington.edu/~saurabh/YMFWeb/YMFInput.pl
Finds novel transcription factor binding sites by searching for over-represented (most significant motifs) motifs in DNA sequences.

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