NameLinkDescription
ACTGhttps://prix.hanyang.ac.kractg/search.jspProgram aligning peptide sequences with genes
AlignHUSHhttp://alignhush.mbu.iisc.ernet.in/query.htmlProgram for protein sequence alignment including structure and hydrophobicity information. Accepts peptide sequences as the queries
BALSAhttp://ccmbweb.ccv.brown.edu/balsa.htmlProgram searching  for homology of protein sequences. Accepts peptide sequences as a queries
BLASThttp://dove.embl-heidelberg.de/Blast2
http://www.ebi.ac.uk/Tools/blast/
http://www.xml.nig.ac.jp/wabi/Method?serviceName=Blast&mode=methodList&lang=en
http://sib-blast.osc.edu/		Program for sequence alignments analysis between proteins. Tool sufficient for alignments between protein and peptide sequences. The program screens protein sequence databases for fragments with sequences similar to the peptide sequence submitted as a query
BLAST KOALAhttp://www.kegg.jp/blastkoala/  Tool for protein sequence alignments, associated with KEGG database. Accepts peptide sequences as a query.
BSBBhttp://bioserver1.physics.iisc.ernet.in/bssb/BLAST program version screening Protein Data Bank and displaying structures of proteins similar to this submitted as a  query
CD-HIThttp://weizhongli-lab.org/cd-hit/Server for comparing and clustering amino acid sequences.
CLUSTAL Whttp://www.ebi.ac.uk/clustalw/;
http://www.ddbj.nig.ac.jp/search
http://www.xml.nig.ac.jp/wabi/Method?serviceName=ClustalW&mode=methodList&lang=en		Program designed for multiple sequence alignments between proteins and peptides
COBALThttp://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi?CMD=WebProgram for multiple sequence alignments. Accepts peptide sequences as a queries
COMAhttp://www.ibt.lt/en/laboratories/bioinfo_en/software/coma.htmlServer for protein distant homology search. Accepts peptide sequences as the queries
DIALIGN-TXhttp://dialign-tx.gobics.de/Program for multiple sequence alignments. Accepts peptide sequences as the queries
FASTAhttp://www.ebi.ac.uk/fasta33/
http://www.xml.nig.ac.jp/wabi/Method?serviceName=Fasta&mode=methodList&lang=en		Program for sequence alignments analysis between proteins. Tool sufficient for alignments between protein and peptide sequences
FSAhttp://orangutan.math.berkeley.edu/fsa/Program for sequence alignments
GGSEARCHhttp://www.ebi.ac.uk/Tools/fasta33/index.html?program=GGSEARCHProgram for sequence alignments analysis between proteins. Tool sufficient for alignments between protein and peptide sequences
GUIDANCEhttp://guidance.tau.ac.il/Server for assessing alignment confidence scores
GUIDANCE2http://guidance.tau.ac.il/ver2/Server for assessing alignment confidence scores
HMMERhttp://www.ebi.ac.uk/Tools/hmmer/Program for sequence alignments analysis between proteins. Tool sufficient for alignments between peptide (at least 12 amino acid residues) and protein sequences
HSA/HSSftp://ftp.landfood.ubc.ca/foodsci/HSA/
HSS software is selected by clicking on “go to homo ver” option (see the user instruction available on the website)		HSA – homology similarity analysis computes pattern similarity constants and average side chain property index values of segments in sequences;
HSS – homology similarity search, a step-wise program initiated from N-terminus of query sequences by shifting the reference segment towards C-terminus. Software based on similarity of segments in terms of similarity constant and average property values compared to template sequences
IBIVUhttp://www.ibi.vu.nl/Server providing access to programs aligning amino acid sequences
iSPIDER Centralhttp://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.plProgram finding information about proteins being precursors of identified peptides.
iPTMnethttps://research.bioinformatics.udel.edu/peptidematch/index.jspTool for matching peptide and protein sequences and protein sequence alignments
Kalignhttp://msa.cgb.ki.se;
http://www.ebi.ac.uk/Tools/kalign/		Program designed for multiple sequence alignments between proteins and peptides
KalignPhttp://kalignp.cbr.su.seProgram designed for multiple sequence alignments between proteins and peptides
KMADhttp://www.cmbi.ru.nl/kmad/Program designed to aligne sequences of intrinsically disordered protein
LabWorm Protein alignment & structurehttps://labworm.com/category/protein-peptide/protein-alignment-structureWebsite providing access to programs for protein sequence alignments
Lalignhttp://www.ch.embnet.org/software/LALIGN_form.htmlProgram designed for multiple sequence alignments between proteins and peptides. Program is able to construct more than one possible local alignment between two sequences
MAFFThttp://www.ebi.ac.uk/Tools/mafft/index.html
http://toolkit.tuebingen.mpg.de/mafft
http://align.genome.jp/mafft/
http://www.xml.nig.ac.jp/wabi/Method?serviceName=Mafft&mode=methodList&lang=en		Program for construction of multiple alignments between protein or nucleic acid sequences. Accepts also peptide sequences as a queries. Information about update published in 2008
MPI Bioinformatics Toolkithttps://toolkit.tuebingen.mpg.de/  Website providing access to programs for protein and peptide sequence alignments
MS-BLASThttp://genetics.bwh.harvard.edu/msblast/index.html
http://dove.embl-heidelberg.de/Blast2/msblast.html		Program designed for interpretation of mass spectrometric data of proteins with unknown sequences. Also screens protein sequence databases for fragments with sequences similar to the peptide sequence submitted as a query
Multi-Harmonyhttp://www.ibi.vu.nl/programs/shmrwww/Program predicting functional specificity of peptides and proteins from sequence alignments
Musclehttp://www.ebi.ac.uk/Tools/muscle/Program designed for multiple sequence alignments between proteins and peptides
PARALIGNhttp://www.paralign.orgProgram designed for sequence alignments between proteins. Tool sufficient for alignments between protein and peptide sequences. The program screens protein and patented peptide sequence databases for fragments with sequences similar to the peptide sequence submitted as a query
PSI-Searchhttp://www.ebi.ac.uk/Tools/sss/psisearch/Program designed for sequence alignments between proteins. Tool sufficient for alignments between protein and peptide sequences. The program screens protein sequence databases for fragments with sequences similar to the peptide sequence submitted as a query
Pôle Bioinformatique Lyonnais/NPS@http://pbil.univ-lyon1.fr/Server with the access to many programs able to process peptide sequences: e.g. constructing multiple alignments between sequences, secondary structure prediction calculating amino acids composition and profiles of physico-chemical features
RNAKPROPhttp://rankprop.gs.washington.edu/Program designed for sequence alignments between proteins. Tool sufficient for alignments between protein and peptide sequences. The program screens protein sequence databases for fragments with sequences similar to the peptide sequence submitted as a query
SANSParallelhttp://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi  Program for sequence alignments analysis between proteins. Tool sufficient for alignments between peptide (at least 14 amino acid residues) and protein sequences
SATCHMO-JShttp://makana.berkeley.edu/q/satchmo/Program for protein sequence alignments and construction of filogenetic trees. Accepts peptide sequences as the queries
SIAShttp://imed.med.ucm.es/Tools/sias.html  Program calculating identities and similarities between two amino acid sequences
SPEM, SPEM-3Dhttp://sparks.informatics.iupui.edu/index.php?pageLoc=ServicesProgram for sequence alignments including predicted structure information
SPIALhttp://www.mrc-lmb.cam.ac.uk/genomes/spial/Program evaluating specificity of multiple sequence alignments, accepts protein and peptide sequences as the queries
SSEARCHhttp://www.ddbj.nig.ac.jp/search
http://www.ebi.ac.uk/Tools/ssearch/		Program for sequence alignments analysis between proteins. Tool sufficient for alignments between protein and peptide sequences
Tachyonhttp://tachyon.bii.a-star.edu.sg/index.actionProgram for sequence alignments analysis between proteins. Tool sufficient for alignments between protein and peptide sequences. The program screens protein sequence databases for fragments with sequences similar to the peptide sequence submitted as a query
T-Coffee/M-Coffee/Cloud-Coffee/PTChttp://www.tcoffee.org; http://www.ebi.ac.uk/Tools/t-coffee/; http://gcd.udl.cat/ptc; http://tcoffee.crg.cat/apps/tcoffee/do:tmcoffeeProgram designed for multiple sequence alignments between proteins and peptides
TCShttp://tcoffee.crg.cat/apps/tcoffee/do:coreProgram for evaluation of reliability of sequence alignments
Unipepthttp://unipept.ugent.be/apidocsProgram for alignments between short peptides, released by trypsin, and proteins. Finds fragments identical with query peptides
webPRANKhttp://www.ebi.ac.uk/goldman-srv/webprank/Program for protein sequence alignment and phylogenetic tree construction. Accepts peptide sequences as the queries