| 1) Sequence similarity search
|
|
1.
|
BLAST: Basic Local Alignment Search Tool |
http://www.ncbi.nlm.nih.gov/BLAST/
|
BLASTp is used for finding similar sequences in protein databases |
|
2.
|
HHpred |
ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/
|
Protein homology detection by HMM-HMM comparison |
| 2) Physicochemical characterization
|
|
3.
|
ExPASy – ProtParam tool |
http://web.expasy.org/protparam/
|
Used for computation of various physical and chemical parameters |
| 3) Sub-cellular localization
|
|
4.
|
PSORT B |
http://www.psort.org/psortb
|
PSORTb attained an overall precision of 97% |
|
5.
|
PSLpred |
http://www.imtech.res.in/raghava/pslpred/
|
The overall accuracy of PSLpred is 91.2%. |
|
6.
|
CELLO |
http://cello.life.nctu.edu.tw
|
The overall accuracy of CELLO is 91%. |
|
7.
|
SignalP |
http://www.cbs.dtu.dk/services/SignalP/
|
Predict signal peptide cleavage sites |
|
8.
|
SecretomeP |
http://www.cbs.dtu.dk/services/SecretomeP/
|
Predict bacterial non-classical secretion |
|
9.
|
TMHMM |
http://www.cbs.dtu.dk/services/TMHMM/. |
Predict membrane topology |
|
10.
|
HMMTOP |
http://www.enzim.hu/hmmtop/
|
Predict transmembrane topology |
| 4) Sequence alignment
|
|
11.
|
PRALINE (PRofile ALIgNEment) |
http://ibivu.cs.vu.nl/programs/pralinewww/
|
Integrates homology-extended and secondary structure information for multiple sequence alignment |
| 5) Protein classification
|
|
12.
|
Pfam |
http://pfam.sanger.ac.uk/. |
Collection of multiple protein-sequence alignments and HMMs |
|
13.
|
CATH (Class, Architecture, Topology, Homology) |
http://www.cathdb.info/
|
Hierarchical domain classification of PDB structures |
|
14.
|
SUPERFAMILY |
http://supfam.cs.bris.ac.uk/SUPERFAMILY
|
Based on SCOP database |
|
15.
|
SYSTERS |
http://systers.molgen.mpg.de
|
- |
|
16.
|
SVMProt |
http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi. |
SVM based classification with accuracy of 69.1–99.6% |
|
17.
|
CDART (The Conserved Domain Architecture Retrieval Tool) |
http://www.ncbi.nlm.nih. gov/Structure/Lexington/Lexington.cgi. |
NCBI Entrez Protein Database search of domain architecture |
|
18.
|
PANTHER (Protein Analysis THrough Evolutionary Relationships) |
http://www.pantherdb.org
|
Classification based on HMM-HMM search |
|
19.
|
ProtoNet |
http://www.protonet.cs.huji.ac.il
|
Based on automatic hierarchical clustering of the protein sequences |
|
20.
|
SMART (Simple Modular Architecture Research Tool) |
http://smart.embl.de/
|
Identification and annotation of protein domains |
| 6) Motif Discovery
|
|
21.
|
InterProScan |
http://www.ebi.ac.uk/InterProScan/
|
Searches InterPro for motif discovery |
|
22.
|
MOTIF |
http://www.genome.jp/tools/motif/
|
Japanese GenomeNet service for motif discovery |
|
23.
|
MEME Suite |
http://meme.nbcr.net
|
- |
| 7) Clustering
|
|
24.
|
CLUSS |
http://prospectus.usherbrooke.ca/cluss/
|
Clustering on the basis of Substitution Matching Similarity (SMS) |
| 8) Virulence factor analysis
|
|
25.
|
VirulentPred |
http://bioinfo.icgeb.res.in/virulent/
|
Accomplish an accuracy of 81.8% |
|
26.
|
VICMpred |
http://www.imtech.res.in/raghava/vicmpred/
|
Attain accuracy of 70.75%. |
| 9) Protein-protein interaction
|
|
27.
|
STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) |
http://string-db.org
|
Version –9.05 |
