Minimotif Miner: A Computational Tool to Investigate Protein Function, Disease, and Genetic Diversity

  title={Minimotif Miner: A Computational Tool to Investigate Protein Function, Disease, and Genetic Diversity},
  author={Martin R. Schiller},
  journal={Current Protocols in Protein Science},
  • M. Schiller
  • Published 1 May 2007
  • Biology, Computer Science
  • Current Protocols in Protein Science
The Minimotif Miner Web site contains information on several hundred short functional motifs in a single database, and allows the user to search protein queries for the presence of these motifs. Scoring based on evolutionary conservation, protein surface prediction, and motif frequency can be used in conjunction with other motif programs and the known biology of the query to reduce false‐positive predictions and select short motifs for experimental pursuit. 

Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences

The third release of the MnM database is reported, which has now grown 60-fold to approximately 300 000 minimotifs, and a new set of false-positive filters and linear regression scoring that vastly enhance minimotIF prediction accuracy on a test data set are summarized.

Minimotif miner 2nd release: a database and web system for motif search

This work revised MnM by expanding the database more than 10-fold to approximately 5000 motifs and standardized the motif function definitions, and the web-application user interface has been redeveloped with new features including improved navigation, screencast-driven help, support for alias names and expanded SNP analysis.

C terminus of the P2X7 receptor: treasure hunting

The role of the P2X7R C terminus in regards to receptor function is discussed, the specific domains and motifs found therein are described and compared with others proteins to discover predicted domains or sites of PTM are compared.

The EFF-1A Cytoplasmic Domain Influences Hypodermal Cell Fusions in C. elegans But Is Not Dependent on 14-3-3 Proteins

Deletion of the EFF-1A endodomain noticeably affects the timing of hypodermal cell fusions in vivo, and the two 14-3-3 proteins in C. elegans, PAR-5 and FTT-2, may regulate either localization or fusion-inducing activity of EFF-0, highlighting the necessity of tight fusogen regulation for proper development.

A Unified Bug Testing Software for Biological and Other Systems

This paper reports one such bug testing software that is created for the MnM web system for motif search and feels that the architecture it has employed is generic and can be applied to other software systems as well.



Minimotif Miner: a tool for investigating protein function

A motif database comprising 312 unique motifs and a web-based tool for identifying motifs in proteins are constructed and functional motifs predicted by MnM are validated by analyzing thousands of confirmed examples and by confirming prediction of previously unidentified 14-3-3 motifsIn EFF-1.

ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins

ELM, the Eukaryotic Linear Motif server at, is a new bioinformatics resource for investigating candidate short non-globular functional motifs in eukaryosis proteins, aiming to fill the void in bio informatics tools.

Recent improvements to the SMART domain-based sequence annotation resource

The SMART database now contains information on intrinsic sequence features such as transmembrane regions, coiled-coils, signal peptides and internal repeats and new advanced queries provide direct access to the SMART relational database using SQL.

trEST, trGEN and Hits: access to databases of predicted protein sequences

Three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future are described, especially to biologists not having access to a powerful local bioinformatics environment.

The PROSITE database, its status in 2002

The PROSITE database consists of biologically significant patterns and profiles designed in such a way that with appropriate computational tools it can rapidly and reliably help to determine to which known family of proteins (if any) a new sequence belongs, or which known domain(s) it contains.

Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs

Scansite identifies short protein sequence motifs that are recognized by modular signaling domains, phosphorylated by protein Ser/Thr- or Tyr-kinases or mediate specific interactions with protein or phospholipid ligands, allowing segments of biological pathways to be constructed in silico.

CDD: a curated Entrez database of conserved domain alignments

The Conserved Domain Database (CDD), which mirrors the publicly available domain alignment collections SMART and PFAM, and now also contains alignment models curated at NCBI, is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE(R).

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.

Current bioinformatics tools in genomic biomedical research (Review).

In this review, the basic bioinformatics tools for genomic research such as: genomic databases, genome browsers, tools for sequence alignment, single nucleotide polymorphism (SNP) databases, tool for ab initio gene prediction, expression databases, and algorithms for promoter prediction are described.