Probability-based protein identification by searching sequence databases using mass spectrometry data.

Several algorithms have been described in the literature for protein identification by searching a sequence database using mass spectrometry data. In some approaches, the experimental data are peptide molecular weights from the digestion of a protein by an enzyme. Other approaches use tandem mass spectrometry (MS/MS) data from one or more peptides. Still others combine mass data with amino acid sequence data. We present results from a new computer program, Mascot, which integrates all three types of search. The scoring algorithm is probability based, which has a number of advantages: (i) A simple rule can be used to judge whether a result is significant or not. This is particularly useful in guarding against false positives. (ii) Scores can be compared with those from other types of search, such as sequence homology. (iii) Search parameters can be readily optimised by iteration. The strengths and limitations of probability-based scoring are discussed, particularly in the context of high throughput, fully automated protein identification.

PROMISE: a database of information on prosthetic centres and metal ions in protein active sites.

The PROMISE (Prosthetic centres andmetalions in protein activesites) database aims to gather together comprehensive sequence, structural, functional and bibliographic information on proteins which possess prosthetic centres, with an emphasis on active site structure and function. The database is available on the World Wide Web at http://bioinf.leeds.ac.uk/promise/

The PRINTS database of protein fingerprints: a novel information resource for computational molecular biology.

PRINTS is a compendium of protein motif fingerprints derived from the OWL composite sequence database. Fingerprints are groups of motifs within sequence alignments whose conserved nature allows them to be used as signatures of family membership. Fingerprints inherently offer improved diagnostic reliability over single motif methods by virtue of the mutual context provided by motif neighbors. To date, 650 fingerprints have been constructed and stored in PRINTS, the size of which has doubled in the last 2 years. The current version, 14.0, encodes 3500 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. The database is now accessible via the UCL Bioinformatics Server on http:@ www.biochem.ucl.ac.uk/bsm/dbbrowser/. We describe here progress with the database, its compilation and interrogation software, and its Web interface.

XFINGER: a tool for searching and visualising protein fingerprints and patterns.

A tool for searching pattern and fingerprint databases is described. Fingerprints are groups of motifs excised from conserved regions of sequence alignments and used for iterative database scanning. The constituent motifs are thus encoded as small alignments in which sequence information is maximised with each database pass; they therefore differ from regular-expression patterns, in which alignments are reduced to single consensus sequences. Different database formats have evolved to store these disparate types of information, namely the PROSITE dictionary of patterns and the PRINTS fingerprint database, but programs have not been available with the flexibility to search them both. We have developed a facility to do this: the system allows query sequences to be scanned against either PROSITE, the full PRINTS database, or against individual fingerprints. The results of fingerprint searches are displayed simultaneously in both text and graphical windows to render them more tangible to the user. Where structural coordinates are available, identified motifs may be visualised in a 3D context. The program runs on Silicon Graphics machines using GL graphics libraries and on machines with X servers supporting the PEX extension: its use is illustrated here by depicting the location of low-density lipoprotein-binding (LDL) motifs and leucine-rich repeats in a mosaic G-protein-coupled receptor (GPCR).

VISTAS: a package for VIsualizing STructures and sequences of proteins.

VISTAS is a suite of programs for protein sequence and structure analysis. The system allows the simultaneous display, in separate windows, of multiple sequence alignments, of known or model 3D structures, and of 2D graphic representations of sequence and/or alignment properties. The displays are fully integrated, and therefore manipulations in one window can be reflected in each of the others. Beyond its display facilities, VISTAS brings together a number of existing tools under a single, user-friendly umbrella: these include a fully functional interactive color alignment procedure, conserved motif selection, a range of database-scanning routines, and interactive access to the OWL composite sequence database and to the PRINTS protein fingerprint database. Exploration of the sequence database is thus straightforward, and predefined structural motifs from the fingerprint database may be readily visualized. Of particular note is the ability to calculate conservation criteria from sequence alignments and to display the information in a 3D context: this renders VISTAS a powerful tool for aiding mutagenesis studies and for facilitating refinement of molecular models.

A cross-cultural comparison of the use of a Gestalt perceptual strategy.

The ability to discriminate whether pictured box shapes (parallelopipeds) are projections of three-dimensional rectangular forms has been demonstrated by Perkins and Cooper in US populations and interpreted as a symptom of a general Gestalt strategy in perception. Deregowski suggested earlier that this perceptual strategy might not appear as strongly in less 'carpentered' cultures, among perceivers less familiar with Western modes of depiction. A study is reported in which the performance on the discrimination by US children in grades 1, 4, and 7; and children from Zimbabwe, Africa, in grades 1, 2, 4, and 7--children of less experience with pictures and urban environments--has been examined. All groups evinced the discrimination at high levels of statistical significance. However, the findings disclosed much less accurate performance in the Zimbabwe groups at all grade levels, and no improvement with age either in the US or in Zimbabwe. The absence of improvement argues against an explanation of the difference between the US and Zimbabwe groups in terms of either a carpentered-world hypothesis or a difficulty with picture perception, at least when those interpretations are taken in their simplest forms.

How good a bet is good form?

'Good form' theories of perception leave some latitude concerning how casually or cautiously order is imposed on the stimulus. Exploring this issue, the present experiment introduced a series of figures admitting up to three alternative 'good' readings. Eight college students estimated two angles in each of fifty-six pictured spatial forms. Theory predicted that geometrical regularities of rectangularity and symmetry would dominate their estimates. But a regularity would rarely appear when inconsistent with projective geometry and the given figure. The accuracy of subjects' estimates was also assessed. The results confirmed the hypotheses at high significance levels, arguing that such figures are interpreted through an order-imposing process restrained by projective geometry, and that subjects could make roughly accurate estimates based on the imposed order. Parallels with computer scene analysis are discussed. It is concluded that perceptual presumption of certain 'good forms' runs little risk of misinterpreting the stimulus.

Coding position in a sequence by rhythmic grouping.

It has been suggested that a perceived rhythmic organization may mediate remembering musical and other stimuli. This experiment examined whether or not Ss could register and remember position in a sequence using rhythmic grouping. Sixteen Ss heard tapped sequences 24-63 beats long, accented to encourage grouping by 4s. Ss tapped responses revealing whether or not they remembered the sequence length-the last tap's position. Significantly more incorrect responses were off by multiples of 4 beats than by adjacent amounts; these frequent errors of whole rhythmic groups of 4 showed that Ss coded sequence length rhythmically. Ss proved 53% accurate over four response conditions, with individual's scores ranging from 8% to 87%. It was concluded that Ss could count with rhythmic hierarchies, essentially equivalent to counting with a nonstandard number base, to code sequential position.