Simulating complex traits influenced by genes with fuzzy-valued effects in pedigreed populations

MOTIVATION: Methods involving fuzzy theory have been rarely applied to genetics. We present an open platform for experimentation with fuzzy numbers as a tool to represent imprecise phenotypes in genetic modeling. RESULTS: A C++ library for simulation of genetic information transmission is introduced. The study of genetic linkage was its first goal, though a design so general as possible has been meant. Fuzzy-valued phenotypes are handled by means of fuzzy numbers. AVAILABILITY: ftp://carleos.etsiig.uniovi.es/pub/falin ftp://fisher.ciencias.uniovi.es/pub/falin ftp://bellman.ciencias.uniovi.es/pub/falin Licensed under the GNU General Public License version 2 (see http://www.gnu.org/licenses/gpl.html).     

mmsearch: a motif arrangement language and search program.

This paper presents a language for describing arrangements of motifs in biological sequences, and a program that uses the language to find the arrangements in motif match databases. The program does not by itself search for the constituent motifs, and is thus independent of how they are detected, which allows it to use motif match data of various origins. AVAILABILITY: The program can be tested online at http://hits.isb-sib.ch and the distribution is available from ftp://ftp.isrec.isb-sib.ch/pub/software/unix/mmsearch-1.0.tar.gz CONTACT: Thomas.Junier@isrec.unil.ch SUPPLEMENTARY INFORMATION: The full documentation about mmsearchis available from http://hits.isb-sib.ch/~tjunier/mmsearch/doc.     

MedPost: a part-of-speech tagger for bioMedical text

SUMMARY: We present a part-of-speech tagger that achieves over 97% accuracy on MEDLINE citations. AVAILABILITY: Software, documentation and a corpus of 5700 manually tagged sentences are available at ftp://ftp.ncbi.nlm.nih.gov/pub/lsmith/MedPost/medpost.tar.gz     

Swissknife - 'lazy parsing' of SWISS-PROT entries.

SUMMARY: We present Swissknife, a set of Perl modules which provides a fast and reliable object-oriented interface to parsing and modifying files in SWISS-PROT format. AVAILABILITY: The Swissknife modules are available at ftp://ftp.ebi.ac. uk/pub/software/swissprot/. CONTACT: hhe@ebi.ac.uk     

Clustal W and Clustal X version 2.0

SUMMARY: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. AVAILABILITY: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/     

VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL

SUMMARY: The program varsplic.pl uses information present in the SWISS-PROT and TrEMBL databases to create new records for alternatively spliced isoforms. These new records can be used in similarity searches. AVAILABILITY: The program is available at ftp://ftp.ebi.ac.uk/pub/software/swissprot/, together with regularly updated output files. CONTACT: pkersey@ebi.ac.uk     

MOSAIC: segmenting multiple aligned DNA sequences

MOSAIC is a set of tools for the segmentation of multiple aligned DNA sequences into homogeneous zones. The segmentation is based on the distribution of mutational events along the alignment. As an example, the analysis of one repeated sequence belonging to the subtelomeric regions of the yeast genome is presented. AVAILABILITY: Free access from ftp://ftp.biomath.jussieu.fr/pub/papers/MOSAIC     

rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control

rh_tsp_map is a software package for computing radiation hybrid (RH) maps and for integrating physical and genetic maps. It solves the central mapping instances by reducing them to the traveling salesman problem (TSP) and using a modification of the CONCORDE package to solve the TSP instances. We present some of the features added between the initial rh_tsp_map version 1.0 and the current version 3.0, emphasizing the automation of many steps and addition of various checks designed to find problems with the input data. Iterations of improved input data followed by fast re-computation of the maps improves the quality of the final maps. AVAILABILITY: rh_tsp_map source code and documentation including a tutorial is available at ftp://ftp.ncbi.nih.gov/pub/agarwala/rhmapping/rh_tsp_map.tar.gz. CONCORDE modified for RH mapping is available in the directory http://www.isye.gatech.edu/~wcook/rh/. The QSopt library needed for CONCORDE is available at http://www2.isye.gatech.edu/~wcook/qsopt/downloads/downloads.htm     

KIND-a non-redundant protein database

SUMMARY: KIND (Karolinska Institutet Nonredundant Database) is a protein database where identical sequences, both full length and partial, have been removed. The database contains nearly 274 900 sequences, half of which originate from the protein sequence databases Swissprot and PIR, while the other half come from translated open reading frames in GenPept and TrEMBL. AVAILABILITY: KIND is downloadable from ftp://ftp.mbb.ki.se/pub/KIND.     

EC_oligos: automated and whole-genome primer design for exons within one or between two genomes

SUMMARY: EC_oligos designs oligonucleotides (oligos) from exons of annotated genomic sequence information. It can automatically and rapidly select oligos that are conserved between two sets of sequence data, and can pair up oligos for use as PCR primers. It can do this on a whole-genome scale and according to user-defined criteria. AVAILABILITY: The source code, executable program and user manual are available at ftp://ftp.ebi.ac.uk/pub/software/dos/EC_oligos/.     

InterProScan--an integration platform for the signature-recognition methods in InterPro

InterProScan is a tool that scans given protein sequences against the protein signatures of the InterPro member databases, currently--PROSITE, PRINTS, Pfam, ProDom and SMART. The number of signature databases and their associated scanning tools as well as the further refinement procedures make the problem complex. InterProScan is designed to be a scalable and extensible system with a robust internal architecture. AVAILABILITY: The Perl-based InterProScan implementation is available from the EBI ftp server (ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/) and the SRS-basedInterProScan is available upon request. We provide the public web interface (http://www.ebi.ac.uk/interpro/scan.html) as well as email submission server (interproscan@ebi.ac.uk).     

EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database

The submission of multiple sequence alignment data to EMBL has grown 30-fold in the past 10 years, creating a problem of archiving them. The EBI has developed a new public database of multiple sequence alignments called EMBL-Align. It has a dedicated web-based submission tool, Webin-Align. Together they represent a comprehensive data management solution for alignment data. Webin-Align accepts all the common alignment formats and can display data in CLUSTALW format as well as a new standard EMBL-Align flat file format. The alignments are stored in the EMBL-Align database and can be queried from the EBI SRS (Sequence Retrieval System) server. AVAILABILITY: Webin-Align: http://www.ebi.ac.uk/embl/Submission/align_top.html, EMBL-Align: ftp://ftp.ebi.ac.uk/pub/databases/embl/align, http://srs.ebi.ac.uk/     

VISTRAJ: exploring protein conformational space

VISTRAJ is an application which allows 3D visualization, manipulation and editing of protein conformational space using probabilistic maps of this space called 'trajectory distributions'. Trajectory distributions serve as input to FOLDTRAJ which samples protein structures based on the represented conformational space. VISTRAJ also allows FOLDTRAJ to be used as a tool for homology model creation, and structures may be generated containing post-translationally modified amino acids. AVAILABILITY: Binaries are freely available for non-profit use as part of the FOLDTRAJ package at ftp://ftp.mshri.on.ca/pub/TraDES/foldtraj/.     

The DOMON domains are involved in heme and sugar recognition

We expand the functionally uncharacterized DOMON domain superfamily to identify several novel families, including the first prokaryotic representatives. Using several computational tools we show that it is involved in ligand binding--either as heme- or sugar-binding domains. We present evidence that the DOMON domain along with the DM13 domain comprises a novel electron-transfer system potentially involved in oxidative modification of animal cell-surface proteins. Other novel versions might function as sugar sensors of histidine kinases of bacterial two component systems. Supplementary information: Supplementary data are available at Bioinformatics online and also at ftp://ftp.ncbi.nih.gov/pub/aravind/domon/.     

iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions

SUMMARY: There are many resources that contain information about binary interactions between proteins. However, protein interactions are defined by only a subset of residues in any protein. We have implemented a web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. This detailed knowledge relies on the fact that there are a large number of multidomain proteins and protein complexes being deposited in the structure databases. The resource called iPfam is hosted within the Pfam UK website. Most resources focus on the interactions between proteins; iPfam includes these as well as interactions between domains in a single protein. AVAILABILITY: iPfam is available on the Web for browsing at http://www.sanger.ac.uk/Software/Pfam/iPfam/; the source-data for iPfam is freely available in relational tables via the ftp site ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/.     

PROF_ PAT 1.3: updated database of patterns used to detect local similarities

MOTIVATION: When analysing novel protein sequences, it is now essential to extend search strategies to include a range of 'secondary' databases. Pattern databases have become vital tools for identifying distant relationships in sequences, and hence for predicting protein function and structure. The main drawback of such methods is the relatively small representation of proteins in trial samples at the time of their construction. Therefore, a negative result of an amino acid sequence comparison with such a databank forces a researcher to search for similarities in the original protein banks. We developed a database of patterns constructed for groups of related proteins with maximum representation of amino acid sequences of SWISS-PROT in the groups. RESULTS: Software tools and a new method have been designed to construct patterns of protein families. By using such method, a new version of databank of protein family patterns, PROF_ PAT 1.3, is produced. This bank is based on SWISS-PROT (r1.38) and TrEMBL (r1.11), and contains patterns of more than 13 000 groups of related proteins in a format similar to that of the PROSITE. Motifs of patterns, which had the minimum level of probability to be found in random sequences, were selected. Flexible fast search program accompanies the bank. The researcher can specify a similarity matrix (the type PAM, BLOSUM and other). Variable levels of similarity can be set (permitting search strategies ranging from exact matches to increasing levels of 'fuzziness'). AVAILABILITY: The Internet address for comparing sequences with the bank is: http://wwwmgs.bionet.nsc.ru/mgs/programs/prof_pat/. The local version of the bank and search programs (approximately 50 Mb) is available via ftp: ftp://ftp.bionet.nsc. ru/pub/biology/vector/prof_pat/, and ftp://ftp.ebi.ac. uk/pub/databases/prof_pat/. Another appropriate way for its external use is to mail amino acid sequences to bachin@vector.nsc.ru for comparison with PROF_ PAT 1.3.     

LIGAND: database of chemical compounds and reactions in biological pathways

LIGAND is a composite database comprising three sections: COMPOUND for the information about metabolites and other chemical compounds, REACTION for the collection of substrate–product relations representing metabolic and other reactions, and ENZYME for the information about enzyme molecules. The current release (as of September 7, 2001) includes 7298 compounds, 5166 reactions and 3829 enzymes. In addition to the keyword search provided by the DBGET/LinkDB system, a substructure search to the COMPOUND and REACTION sections is now available through the World Wide Web (http://www.genome.ad.jp/ligand/). LIGAND may be also downloaded by anonymous FTP (ftp://ftp.genome.ad.jp/pub/kegg/ligand/).     

MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs.

MEDUSA is a tool for automatic selection and visual assessment of PCR primer pairs, developed to assist large scale gene expression analysis projects. The system allows specification of constraints of the location and distances between the primers in a pair. For instance, primers in coding, non-coding, exon/intron-spanning regions might be selected. Medusa applies these constraints as a filter to primers predicted by three external programs, and displays the resulting primer pairs graphically in the Blixem (Sonnhammer and Durbin, COMPUT: Appl. Biosci. 10, 301-307, 1994; http://www.cgr.ki.se/cgr/groups/sonnhammer/Blixem.html) viewer. AVAILABILITY: The MEDUSA web server is available at http://www.cgr.ki.se/cgr/MEDUSA. The source code and user information are available at ftp://ftp.cgr.ki.se/pub/prog/medusa.     

Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes.

Promoter Extraction from GenBank (PEG) extracts promoter sequences for large sets of genes using information present in GenBank. For a gene whose promoter sequence is not found, PEG will attempt to extract promoter sequences of the orthologous genes instead. AVAILABILITY: It is freely available to academic users at ftp://cshl.org/pub/science/mzhanglab/theresa/. CONTACT: zhangt@cshl.org; mzhang@cshl.org     

Assembly of fingerprint contigs: parallelized FPC

SUMMARY: One of the more common uses of the program FingerPrint Contigs (FPC) is to assemble random restriction digest 'fingerprints' of overlapping genomic clones into contigs. To improve the rate of assembling contigs from large fingerprint databases we have adapted FPC so that it can be run in parallel on multiple processors and servers. The current version of 'parallelized FPC' has been used in our laboratory to assemble mammalian BAC fingerprint databases, each containing more than 300000 BAC fingerprints. AVAILABILITY: This parallelized version of FPC is available under the GNU GPL licence, and can be downloaded from ftp://ftp.bcgsc.bc.ca/pub/fpcd.