HPMV: human protein mutation viewer - relating sequence mutations to protein sequence architecture and function changes.
Next-generation sequencing advances are rapidly expanding the number of human mutations to be analyzed for causative roles in genetic disorders. Our Human Protein Mutation Viewer (HPMV) is intended to explore the biomolecular mechanistic significance of non-synonymous human mutations in protein-coding genomic regions. The tool helps to assess whether protein mutations affect the occurrence of sequence-architectural features (globular domains, targeting signals, post-translational modification sites, etc.). As input, HPMV accepts protein mutations - as UniProt accessions with mutations (e.g. HGVS nomenclature), genome coordinates, or FASTA sequences. As output, HPMV provides an interactive cartoon showing the mutations in relation to elements of the sequence architecture. A large variety of protein sequence architectural features were selected for their particular relevance to mutation interpretation. Clicking a sequence feature in the cartoon expands a tree view of additional information including multiple sequence alignments of conserved domains and a simple 3D viewer mapping the mutation to known PDB structures, if available. The cartoon is also correlated with a multiple sequence alignment of similar sequences from other organisms. In cases where a mutation is likely to have a straightforward interpretation (e.g. a point mutation disrupting a well-understood targeting signal), this interpretation is suggested. The interactive cartoon can be downloaded as standalone viewer in Java jar format to be saved and viewed later with only a standard Java runtime environment. The HPMV website is: http://hpmv.bii.a-star.edu.sg/ .
Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore 138671, Singapore.
Westley Arthur
WA
Sherman
Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore 138671, Singapore.
Durga Bhavani
DB
Kuchibhatla
Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore 138671, Singapore.
Vachiranee
V
Limviphuvadh
Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore 138671, Singapore.|School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore.
Sebastian
S
Maurer-Stroh
Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore 138671, Singapore.
Birgit
B
Eisenhaber
Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix, Singapore 138671, Singapore.|Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive 4, Singapore 117597, Singapore.|School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553, Singapore.
Frank
F
Eisenhaber
D000595:Amino Acid Sequence; D019295:Computational Biology; D003196:Computer Graphics; D017124:Conserved Sequence; D054707:Cyclic Nucleotide Phosphodiesterases, Type 6 / Q000235:genetics; D030562:Databases, Protein / Q000706:statistics & numerical data; D005136:Eye Proteins / Q000235:genetics; D019204:GTP-Binding Proteins; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics; D008565:Membrane Proteins / Q000235:genetics; D009154:Mutation; D011506:Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D012984:Software
D005136:Eye Proteins; D047908:Intracellular Signaling Peptides and Proteins; D008565:Membrane Proteins; D011506:Proteins; C072178:RP2 protein, human; D054707:Cyclic Nucleotide Phosphodiesterases, Type 6; C517431:PDE6B protein, human; D019204:GTP-Binding Proteins
Human protein mutations; clinical genome sequencing; genomic variation; protein function; protein sequence architecture