Protein Analysis

Sequence Information

— Alignment

— Analysis

— Similarity Searching

Alignment

• ALIGN
  Compendium of sequence alignments intended as a companion resource to PRINTS
• CINEMA
  Colour INteractive Editor for Multiple Alignments. The program allows visualisation and manipulation of both protein and DNA sequences
• DIALIGN
  Construct pairwise and multiple alignments by comparing whole segments of sequences
• EMBL-EBI ClustalW
  Perform multiple DNA or protein sequences alignments
• MultAlin
  Perform multiple sequence alignment with hierarchical clustering
• Pfam
  Search a large collection of multiple sequence alignments and HMM covering many common protein domains and families
• ProDom
  Search and analyze protein domain families
• T-coffee
  Mix sequence and structure information to generate multiple sequence alignments

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Analysis

• BAliBASE
  Evaluate sequence alignment using the benchmark alignment database
• BLOCKS
  Search for ungapped segments corresponding to the most highly conserved regions of proteins
• CHOP
  Dissect proteins into domain-like fragments based on sequence homology
• ClusTr
  Study classification of UniProtKB proteins into groups of related proteins
• COILS
  Predict coil regions in proteins
• Compute pl/Mw
  Compute theoretical pl and Mw for Swiss-Prot and TrEMBL entries or for user entered sequence
• EMBL-EBI Radar
  Find sequence repeats in a protein sequence
• EMBL-EBI SAPS
  Evaluate by statistical criteria a wide variety of protein sequence properties
• NetOGlyc
  Produce neural network predicitions of GalNac O-glycosylation sites in mammalian proteins
• NetPhos
  Produce neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins
• ProtScale
  Find the physico-chemical properties ( molecular wt, polarity, hydrophobicity, etc.) of an amino acid sequence
• SignalP
  Predict signal peptide cleavage sites in amino acid sequences
• Sulfinator
  Predict the presence of tyrosine sulfation sites in protein sequences

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Similarity Searching

• BCM Search Launcher
  Determine protein function for a DNA sequence or find genomic sequence corresponding to a gene
• EMBL-EBI Wise2
  Compare a protein sequence to a genomic DNA sequence, allowing for introns and frame shifting errors
• EMBL-EBI WU-Blast2
  Find regions of protein sequence similarity quickly, with minimum loss of sensitivity
• NCBI BLAST Portal
  Find regions of local similarity between sequences
• NCBI COG
  Generate clusters of orthologous groups by comparing protein sequences encoded within complete genomes

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