Computer applications in the biosciences : CABIOS最新文献

{"title":"PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees.","authors":"N C Grassly, J Adachi, A Rambaut","doi":"10.1093/bioinformatics/13.5.559","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.5.559","url":null,"abstract":"PSeq-Gen will simulate the evolution of protein sequences along evolutionary trees following the procedures previously reported for the DNA sequence simulator Seq-Gen (Sequence-Generator, Rambaut and Grassly, 1997). Statis-tics calculated from these sequences can be used to give expectations under specific null hypotheses of protein evolution. This Monte Carlo simulation approach to testing hypotheses is often termed 'parametric bootstrapping' (see, for example, Efron, 1985; Huelsenbeck et al., 19%; Huelsenbeck and Rannala, 1997), and has many powerful applications, such as testing the molecular clock (Goldman, 1993), detecting recombination (Grassly and Holmes, 1997), and evaluating competing phylogenetic hypotheses (Hillis et al., 19%). Three are mitochondrial each","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 5","pages":"559-60"},"PeriodicalIF":0.0,"publicationDate":"1997-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.5.559","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20296465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PAML: a program package for phylogenetic analysis by maximum likelihood.","authors":"Z Yang","doi":"10.1093/bioinformatics/13.5.555","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.5.555","url":null,"abstract":"PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such as branch lengths in a phylogenetic tree, the transition/transversion rate ratio, the shape parameter of the gamma distribution for variable evolutionary rates at sites, and rate parameters for different genes; (ii) likelihood ratio test of hypotheses concerning sequence evolution, such as rate constancy and independence among sites and rate constancy among lineages (the molecular clock); (iii) calculation of substitution rates at sites and reconstruction of ancestral nucleotide or amino acid sequences; and (iv) phylogenetic tree reconstruction by maximum likelihood and Bayesian methods. The strength of PAML, in comparison with other phylogenetic packages currently available, is its implementation of a variety of evolutionary models. These include several models of variable evolutionary rates among sites, models for combined analyses of multiple gene sequence data and models for amino acid sequences. Multifurcating trees are supported, as well as trees in which some sequences are ancestral to some others. A heuristic tree search algorithm (star decomposition) is used in the package, but tree making is not a strong point of the current version, although work is under way to implement efficient search algorithms. Major programs in the package, as well as the types of analyses they perform, are listed in Table 1. More details are available in the documentation included in the package, written using Microsoft Word. PAML is distributed free of charge for academic use only. The package, including ANSI C source codes, documentation, example data sets, and control files, can be obtained by anonymous ftp at mw511.biol.berkeley.edu/pub, or from the Indiana molecular biology ftp site at ftp.bio.indiana.edu under the directory Incoming or molbio/evolve . MAC and PowerMac executables are also available, although DOS executables are not prepared yet. Further information about the package is available from the World Wide Web at","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 5","pages":"555-6"},"PeriodicalIF":0.0,"publicationDate":"1997-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.5.555","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20296463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MACS: automatic counting of objects based on shape recognition.","authors":"J P Rolland, P Bon, D Thomas","doi":"10.1093/bioinformatics/13.5.563","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.5.563","url":null,"abstract":"MACS is a tool for obtaining basic measurements of cell domains and for automatic counting of particles like colloidal gold probes.","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 5","pages":"563-4"},"PeriodicalIF":0.0,"publicationDate":"1997-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.5.563","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20296467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimation of equilibrium constants using automated group contribution methods.","authors":"R G Forsythe,&nbsp;P D Karp,&nbsp;M L Mavrovouniotis","doi":"10.1093/bioinformatics/13.5.537","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.5.537","url":null,"abstract":"<p><strong>Motivation: </strong>Group contribution methods are frequently used for estimating physical properties of compounds from their molecular structures. An algorithm for estimating Gibbs energies of formation through group contribution methods has been automated in an object-oriented framework. The algorithm decomposes compound structures according to a basis set of groups. It permits the use of wildcards and is able to distinguish between ring groups and chain groups that use similar search structures. Past methods relied on manual decomposition of compounds into constituent groups.</p><p><strong>Results: </strong>The software is written in Common LISP and requires < 2 min to estimate Gibbs energies of formation for a database of 780 species of varying size and complexity. The software allows rapid expansion to incorporate different basis sets and to estimate a variety of other physical properties.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 5","pages":"537-43"},"PeriodicalIF":0.0,"publicationDate":"1997-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.5.537","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20296460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A platform-independent graphical user interface for SEQSEE and XALIGN.","authors":"D S Wishart,&nbsp;S Fortin,&nbsp;D R Woloschuk,&nbsp;W Wong,&nbsp;T Rosborough,&nbsp;G Van Domselaar,&nbsp;J Schaeffer,&nbsp;D Szafron","doi":"10.1093/bioinformatics/13.5.561","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.5.561","url":null,"abstract":"SEQSEE (Wishart et cil., 1994a) and XALIGN (Wishart et cil., 1994b) are two text-based, menu-driven programs developed specifically for comprehensive protein sequence analysis. Originally compiled to run on SUN and SGI workstations only, SEQSEE and XALIGN have been distributed to more than 300 laboratories around the world. Both programs have been used in a variety of applications ranging from routine sequence analysis to the identification of previously unknown sequence relationships (Upton et cil., 1992, 1993; Dulhanty and Riordan, 1994). Since releasing these programs, we have received numerous requests asking if they could be ported to additional computer platforms (Macintosh and PC) or if the text-based menus could be replaced with a more friendly graphical user interface (GUI).","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 5","pages":"561-2"},"PeriodicalIF":0.0,"publicationDate":"1997-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.5.561","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20296466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DSC: public domain protein secondary structure predication.","authors":"R D King,&nbsp;M Saqi,&nbsp;R Sayle,&nbsp;M J Sternberg","doi":"10.1093/bioinformatics/13.4.473","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.4.473","url":null,"abstract":"","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 4","pages":"473-4"},"PeriodicalIF":0.0,"publicationDate":"1997-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.4.473","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20224212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"JaMBW 1.1: Java-based Molecular Biologists' Workbench.","authors":"L I Toldo","doi":"10.1093/bioinformatics/13.4.475","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.4.475","url":null,"abstract":"","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 4","pages":"475-6"},"PeriodicalIF":0.0,"publicationDate":"1997-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.4.475","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20224213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid protein fragment search using hash functions based on the Fourier transform.","authors":"T Akutsu,&nbsp;K Onizuka,&nbsp;M Ishikawa","doi":"10.1093/bioinformatics/13.4.357","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.4.357","url":null,"abstract":"<p><strong>Motivation: </strong>Since the protein structure database has been growing very rapidly in recent years, the development of efficient methods for searching for similar structures is very important.</p><p><strong>Results: </strong>This paper presents a novel method for searching for similar fragments of proteins. In this method, a hash vector (a vector of real numbers) is associated with each fixed-length fragment of three-dimensional protein structure. Each vector consists of low-frequency components of the Fourier-like spectrum for the distances between C alpha atoms and the centroid. Then, we can analyze the similarity between fragments by evaluating the difference between hash vectors. The novel aspect of the method is that the following property is proved theoretically: if the root mean square distance between two fragments is small, then the distance between the hash vectors is small. Several variants of this method were compared with a naive method and a previous method using PDB data. The results show that the fastest one among the variants is 18-80 times faster than the naive method, and 3-10 times faster than the previous method.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 4","pages":"357-64"},"PeriodicalIF":0.0,"publicationDate":"1997-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.4.357","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20225047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Visual BLAST and visual FASTA: graphic workbenches for interactive analysis of full BLAST and FASTA outputs under MICROSOFT WINDOWS 95/NT.","authors":"P Durand,&nbsp;L Canard,&nbsp;J P Mornon","doi":"10.1093/bioinformatics/13.4.407","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.4.407","url":null,"abstract":"<p><strong>Motivation: </strong>When routinely analysing protein sequences, detailed analysis of database search results made with BLAST and FASTA becomes exceedingly time consuming and tedious work, as the resultant file may contain a list of hundreds of potential homologies. The interpretation of these results is usually carried out with a text editor which is not a convenient tool for this analysis. In addition, the format of data within BLAST and FASTA output files makes them difficult to read.</p><p><strong>Results: </strong>To facilitate and accelerate this analysis, we present for the first time, two easy-to-use programs designed for interactive analysis of full BLAST and FASTA output files containing protein sequence alignments. The programs, Visual BLAST and Visual FASTA, run under Microsoft Windows 95 or NT systems. They are based on the same intuitive graphical user interface (GUI) with extensive viewing, searching, editing, printing and multithreading capabilities. These programs improve the browsing of BLAST/FASTA results by offering a more convenient presentation of these results. They also implement on a computer several analytical tools which automate a manual methodology used for detailed analysis of BLAST and FASTA outputs. These tools include a pairwise sequence alignment viewer, a Hydrophobic Cluster Analysis plot alignment viewer and a tool displaying a graphical map of all database sequences aligned with the query sequence. In addition. Visual Blast includes tools for multiple sequence alignment analysis (with an amino acid patterns search engine), and Visual FASTA provides a GUI to the FASTA program.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 4","pages":"407-13"},"PeriodicalIF":0.0,"publicationDate":"1997-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.4.407","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20225660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Objectively judging the quality of a protein structure from a Ramachandran plot.","authors":"R W Hooft,&nbsp;C Sander,&nbsp;G Vriend","doi":"10.1093/bioinformatics/13.4.425","DOIUrl":"https://doi.org/10.1093/bioinformatics/13.4.425","url":null,"abstract":"<p><strong>Motivation: </strong>Statistical methods that compare observed and expected distributions of experimental observables provide powerful tools for the quality control of protein structures. The distribution of backbone dihedral angles ('Ramachandran plot') has often been used for such quality control, but without a firm statistical foundation.</p><p><strong>Results: </strong>A new and-simple method is presented for judging the quality of a protein structure based on the distribution of backbone dihedral angles. Inputs to the method are 60 torsion angle distributions extracted from protein structures solved at high resolution; one for each combination of residue type and tri-state secondary structure. Output for a protein is a Ramachandran Z-score, expressing the quality of the Ramachandran plot relative to current state-of-the-art structures.</p>","PeriodicalId":77081,"journal":{"name":"Computer applications in the biosciences : CABIOS","volume":"13 4","pages":"425-30"},"PeriodicalIF":0.0,"publicationDate":"1997-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bioinformatics/13.4.425","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20225662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}