Function

File location

Researcher group address

Similarity search

NCBI nucleotide BLAST

impl\Blast\blastN_ncbi

http://www.ncbi.nlm.nih.gov/blast/

NCBI protein BLAST

impl\Blast\blastP_ncbi

http://www.ncbi.nlm.nih.gov/blast/

Ensebl human blast

impl\Blast\blast_human_ensembl

http://www.ensembl.org/Homo_sapiens/blastview

Proteomes and Genomes Fasta, EBI

impl\Blast\Ebi_fasta.class

http://www.ebi.ac.uk/fasta33/genomes.html

Nucleic acid sequence analysis

NCBI electronic PCR

impl\dna_analysers\E_PCR

http://www.ncbi.nlm.nih.gov/genome/sts/epcr.cgi

Genscan web server at MIT

impl\dna_analysers\geneScanners\GenScan

http://genes.mit.edu/oldGENSCAN.html

Translates a nucleotide sequence to a protein sequence, ExPASy

impl\rna_analysers\rna_translator

http://www.expasy.ch/tools/dna.html

Protein sequence analysis

QuaternaryStructure Predictor: ExperimentalHomodimer Classifier

impl\protein_analysers\Dimers

http://www.mericity.com

Glycosylphosphatidylinositol modification site prediction

impl\protein_analysers\GPI_modification

http://mendel.imp.univie.ac.at/gpi/index_content.html

Integrated search in PROSITE, Pfam, PRINTS and other family and domain databases

impl\protein_analysers\InterPro

http://www.ebi.ac.uk/interpro/scan.html

Prediction of N-terminal N-myristoylation

impl\protein_analysers\Myristoylation

http://mendel.imp.univie.ac.at/myristate/SUPLpredictor.htm

Prediction of mitochondrial targeting sequences

impl\protein_analysers\Predotar

http://www.inra.fr/predotar/

Scans a sequence against PROSITE (allows mismatches); at PBIL

impl\protein_analysers\ProSite

http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_prosite.html

Protein sorting signal prediction

impl\protein_analysers\PSORT

http://psort.nibb.ac.jp/form2.html

Simple Modular Architecture Research Tool; at EMBL

impl\protein_analysers\SMART

http://smart.embl-heidelberg.de/

Prediction of subcellular location, at CBS

impl\protein_analysers\TargetP

http://www.cbs.dtu.dk/services/TargetP/

Prediction of transmembrane regions and protein Orientation (EMBnet-CH)

impl\protein_analysers\TmPred

http://www.ch.embnet.org/software/TMPRED_form.html

NCBI Conserved Domain Search

impl\protein_analysers\CDD_ncbi

http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

Expression profiling in silico

Finding, where the given RNA sequence is expressed (uses NCBI database of expressed sequence tags). This robot depends on the quality and completeness of NCBI EST_human database.

impl\rna_analysers\whereExpressed

http://www.ncbi.nlm.nih.gov/

Sequence downloaders

Reads sequences using Ensembl identifier

impl\sequence_readers\fastaReaderEnsembl

http://www.ensembl.org/Homo_sapiens/

Reads sequence and fasta header from NCBI database using given accession number

impl\sequence_readers\fastaReaderNCBI

http://www.ncbi.nlm.nih.gov/entrez/