Appendix A. Software and Databases for Computational Biology on the Internet

Databases

Motif Search

Secondary Structure Prediction

Other software and information sources

Gene finders and other sequence analysis programs

• Glimmer is a system that uses Interpolated Markov Models (IMMs) to identify coding regions in microbial DNA. IMMs are a generalization of Markov models that allow great flexibility in the choice of the "context"; i.e., how many previous bases to use in predicting the next base. Glimmer has been tested on the complete genomes of H. influenzae, E. coli, H. pylori, M. genitalium, and other genomes, and results to date have proven it to be highly accurate. Glimmer was the principal gene finder for the genomes of B. burgdorferi , T. pallidum, C. trachomatis, C. pneumoniae, D. radiodurans, T. maritima, and others. The complete system, including source code, is available from this site.  A version of the system built for the malaria parasite, GlimmerM, is also available.
• GeneFinding.org is a page with links to most of the latest eukaryotic gene finders.   It has much better links and is more up to date than most of the links below.
  
• GENSCAN is a program designed to predict complete gene structures, including exons, introns, promoter and poly-adenylation signals, in genomic sequences. It differs from the majority of existing gene finding algorithms in that it allows for partial genes as well as complete genes and for the occurrence of multiple genes in a single sequence, on either or both DNA strands. Program versions suitable for vertebrate, nematode (experimental), maize and Arabidopsis sequences are currently available. The vertebrate version also works fairly well for Drosophila sequences. Sequences can be submitted on a web-based form at this site. The GENSCAN Web site is at Stanford University.
• GeneMark is a system for finding genes in bacterial DNA sequences. The algorithm is based on non-homogeneous 5th-order Markov chains, and it was used to locate the genes in the complete genomes of H. influenzae, M. genitalium, and several other complete genomes. The site includes documentation and a Web interface to which sequences can be submitted. This system is at the Georgia Institute of Technology in Atlanta, GA.
• NetPlantGene is at the Technical University of Denmark. The NetPlantGene Web server uses neural networks to predict splice sites in Arabidopsis thaliana DNA. This site also contains programs for other sequence analysis problems as well, such as the recognition of signal peptides. NetPlantGene is to be replaced with NetGene2.
• Repeat Pattern Toolkit (RPT) consists of tools for analyzing repetitive sequences in a genome. RPT takes as input a single sequence in GenBank format, and attempts to find both coding (possible gene duplications, pseudogenes, homologous genes) and non-coding repeats. RPT locates all repeats using a fast Senstive Search Tool (SST). These repeats are evaluated for statistical significance utilizing a sensitive All-PAM search, and their evolutionary distance is estimated. The repeats are classified into families of similar sequences. The classification output is tabulated using perl scripts and plotted using gnuplot. RPT is at the Institute for Biomedical Computing at Washington University in St. Louis.
• SplicePredictor is a program designed to predict donor and acceptor splice sites in maize and Arabidopsis sequences. Sequences can be submitted on a web-based form at this site. The system is at Stanford University.
• TESS (Transcription Element Search Software) is a set of software routines for locating and displaying transcription factor binding sites in DNA sequence. TESS uses the Transfac database as its store of transcription factors and their binding sites. This page is at the University of Pennsylvania's Computational Biology and Informatics Laboratory.
• Genotator, a workbench for automated sequence annotation, provides a flexible, transparent system for automatically running a series of sequence analysis programs on genetic sequences. It also has a graphical display that allows users to view all of the automatically-generated annotations and add their own. Genotator's display allows annotated sequences to be examined at multiple levels of detail, from an overview of the entire sequence down to individual bases. By displaying the aligned output of multiple types of sequence analysis, Genotator provides an intuitive way to identify the significant regions (for example, probable exons) in a sequence. Genotator was developed by Nomi Harris at Lawrence Berkely National Laboratory.
• WebGene (GenView, ORFGene, SpliceView) is Web interface for several coding region recognition programs, including:
  • GenView: a system for protein-coding gene prediction
  • ORFGene: gene structure prediction using information on homologous protein sequences
  • SpliceView: prediction of splicing signals
  • HCpolya: a hamming Clustering Method for Poly-A prediction in eukaryotic genes
  This page is at the Instituto Tecnologie Biomediche Avanzate in Italy.
• The Staden Package contains a wealth of useful programs for sequence assembly, DNA sequence comparison and analysis, protein sequence analysis, and sequencing project quality control. The site is mirrored in several locations around the world. 

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  Databases

• The NCBI Entrez PubMed Browser, at the National Center for Biotechnology Information (NCBI), is the world's largest and most heavily used resource for searching Genbank as well as other NCBI databases.
  
• PhyloFacts is a searchable database of pre-calculated structural and phylogenomic analyses of over 40,000 protein families.  Each family contains a multiple sequence alignment, one or more phylogenetic trees, predicted
  functional subfamilies and 3D structures, PFAM domains, GO annotations, biological literature, predicted critical residues and hidden Markov models; all core data can be downloaded freely from the resource.  Over 1M hidden Markov models (HMMs) for families and subfamilies are provided to enable classification of novel sequences to different levels of a functional hierarchy and for prediction of 3D structure. Users can also perform database queries to retrieve protein families meeting their specified criteria, or simply browse the resource.
• GeneCards is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol as well as selected others. It is especially useful for those who are searching for information working in functional genomics and proteomics. The data is collected with Knowledge Discovery and Data Mining's techniques and accessed by means of proprietary Guidance System that makes more or less intelligent suggestions to the user of where and how the information may be retrieved.
• HHS Sequence Classification. HHS is a database of sequences that have been clustered based on a variety of criteria. The database and clustering algorithms are described in Chapter 6. This Web page, at the Insitute for Biomedical Computing at Washington University in St. Louis, allows one to access classifications by sequence, group listing, structure, and alignment.
• The EpoDB (Erythropoiesis Database) is a database of genes that relate to vertebrate red blood cells. A detailed description of EpoDB can be found on Chapter 5. The database includes DNA sequence, structural features and potential transcription factor binding sites. This Web site is at the University of Pennsylvania's CBIL.
• The LENS (Linking ESTs and their associated Name Space) database links and resolves the names and identifiers of clones and ESTs generated in the I.M.A.G.E. Consortium/WashU/Merck EST project. The name space includes library and clone IDs and names from IMAGE Consortium, EST sequence IDs from Washington University, sequence entry accession numbers from dbEST/NCBI, and library and clone IDs from GDB. LENS allows for querying of IMAGE Consortium data via all the different IDs.
• PDD, the NIMH-NCI Protein-Disease Database is at the Laboratory of Experimental and Computational Biology at the National Cancer Institute. This server is part of the NIMH-NCI Protein-Disease Database project for correlating diseases with proteins observable in serum, CSF, urine and other common human body fluids based on biomedical literature.
• The TRANSFAC Database is at the Gesellschaft für Biotechnologische Forschung mbH (Germany). TRANSFAC is a transcription factor database. It compiles data about gene regulatory DNA sequences and protein factors binding to them. On this basis, programs are developed that help to identify putative promoter or enhancer structures and to suggest their features.
• TransTermHP is a program for predicting transcription terminators in bacteria, and the website has a database of predictions for several hundred genomes.
   

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  Motif Search:

• ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. ELPH has been to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs).
• PROSITE Search Form Allows you to rapidly compare a protein sequence against all patterns stored in the PROSITE pattern database. ScanProsite: Protein against Prosite form allows one to scan a protein sequence (either from SWISS-PROT or provided by the user) for the occurrences of patterns sorted in the PROSITE database. Pattern against SWISS-PROT scans in all of the SWISS-PROT database (including weekly releases) for the occurrence of a pattern that can originate from PROSITE or be provided by the user. (ExPASY)
• Motifs in protein databases program determines if a protein motif is present in a database of protein sequences. This program allows the user to define a protein motif and then determine if a DNA sequence might encode them or if they are present in a protein database. The programs do not search a library of predefined protein motifs. A motif is defined by entering the amino acids of interest at each position.(Alces)
• MatInspectorA tool for the detection of transcription factor binding sites. It is able to locate matches of sequences of unlimited length and compare one, several or all sequences in a sequence file against all or selected subsets of matrices from a library of matrix descriptions of protein binding sites. (GSF)
• MEME - Multiple EM for Motif Elicitation system allows one to discover motifs of highly conserved regions in groups of related DNA or protein sequences and search sequence databases using motifs using MAST: Works by calculating match scores for each sequence. The match scores are converted into various types of p-values and these are used to determine the overall match of the sequence to the group of motifs.(SDSC)
• Regular Expression Searches of Sequence DB using FPAT. This page is designed to search a molecular sequence database (proteins only) for patterns using simple regular expressions.At present, only protein sequence databases are available on the server. (Univ. of Toronto)
• BCM Search Launcher : The Baylor College of Medicine has a variety of biology related search and analysis services including general protein sequence/Pattern searches and Species-Specific Protein Sequence Searches.(HGSC)
• Screening pattern or alignment against PROTEIN databank This method of looking for all pattern entries in PROTEIN databank is almost the same as in PROSITE screening procedure. The one difference is that coincidence of pattern's and fragment's letter could be seen in a broad sense: as a similarity of letters according to a weight matrix selected by the user. (genebee)
• Pattern Searching Proteins: A collection of software tools for protein sequence analysis. PATTINPROT scans a protein sequence or a protein database for one or several patterns. PROSCAN scans a protein sequence for sites/signatures against the PROSITE database.
• PPSEARCH : Prosite Database Searches (sequence against databases of motifs). Allows you to search sequences for motifs or functional patterns in the prosite database (EBI)
• COGnitor: Compare your sequence to COG- Clusters of Orthologous Groups database. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. (NCBI)
• HMMER Sean Eddy: Profile hidden Markov models can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.The advantage of using HMMS is that HMMS have a formal probabilistic basis and can be trained from unaligned sequences, if a trusted alignment isn't yet known. They do however make poor models of RNAs because they cannot describe base pairs. HMMER is a freely distibutable implementation of profile HMM software for protein sequence analysis. (Washington Univ.)
• emotif is a research system that forms motifs for subsets of aligned sequences. Emotif ranks the motifs that it finds by both their specificity and the number of supplied sequences that it covers.(Stanford Bioinformatics Group)
• FunSiteP Promoter Recognition: Recognition and classification of eukaryotic promoters by searching transcription factor binding sites using transcription factor binding site consensi. (GSF)
• SMART Simple Modular Architecture Research Tool: Allows rapid identification and annotation of signalling protein domain sequences. It is able to determine the modular architectures of single sequences or genomes. (EBI)
• SAM : Sequence Alignment and Modeling System using HMM (Hidden Markov Model). SAM is a collection of software tools for creating, refining and using linear HMM for biological sequence analysis. Documentation for SAM can be found here.(Pasteur)
• BioRainbow : Human Promoter Extractor (Prom Extra). The Promextra windows application is designated to solve the problem of extracting promoters fast and simple for given list of genes.
  
  

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  Secondary Structure Prediction:

• THREADER2 is a program for predicting protein tertiary structure by recognizing the correct fold from a library of alternatives. Of course, if a fold similar to the native fold of the protein being predicted is not in the library, then this approach will not succeed. Fortunately, certain folds crop up time and time again, and so fold recognition methods for predicting protein structure can be very effective. In the first prediction contest held at Asilomar, organized by John Moult and colleagues, THREADER correctly identified 8 out of 11 target structures which either globally or locally resembled a previously observed fold. Preliminary analysis of the results from the second competition (CASP2) show that THREADER 2 has shown clear improvement in both fold recognition sensitivity AND sequence-structure alignment accuracy. In CASP2, the new version of THREADER recognized 4 folds correctly out of 6 targets with recognizable structures (including the difficult task of assigning a jelly-roll fold rather than other beta-sandwich topologies for one target). THREADER 2 produced more correct fold predictions (i.e. correct folds ranked at No. 1) than any other method.
• Predict Protein is a service for sequence analysis and structure prediction. Once you submit a protein sequence, PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure, residue solvent accessibility and helical transmembrane regions. (EMBL)
• MultPred - Multpredict Secondary Structure of Multiply Aligned Sequences: This program predicts secondary structure using physicochemical information from a set of aligned sequences and the Garnier secondary structure decision constants. The program requires as input, the sequences, aligned using the AMPS program. (AMPS)
• NNPREDICT Protein Secondary Structure Prediction: A program that predicts the secondary structure type for each residue in an amino acid sequence. The basis of the prediction is a two-layer, feed-forward neural network. NNPREDICT takes as input a protein sequence and returns a secondary structure prediction for each position in the sequence.(UCSF)
• PSA Protein Structure Prediction Server: Predicts probable secondary structures and folding classes for a given amino acid sequence. It performs three types of protein structure/sequence analysis:
  1. Analysis of full length amino acid sequences that are assumed to be monomeric globular, water-soluble proteins consisting of a single domain
  2. Analysis of either complete sequences, or sequence fragments with a minimal set of modelled structural assumptions
  3. Analysis of potential WD-repeat protein family sequences
  (BMERC at Boston University)
• SSCP Secondary Structural Content Prediction computes predictions for the content of helix, strand, and coil for a given protein using the amino acid composition as the only input of inofrmation. The method used by SSCP consists in the application of analytic vector decomposition methods applied on the composition vector of the query protein.
• PREDATOR Secondary structure prediction from fingle or multiple sequences. Takes as input a single protein sequence to be predicted and can optimally use a set of unaligned sequences as additional information to predict the query sequence. PREDATOR does not use multiple sequence alignment, instead it relies on careful pairwise local alignments of the sequences in the set with the query sequence to be predicted. If you supply a set of sequences in the form of a multiple alignment in CLUSTAL or MSF format, the sequences will be used but unaligned. (EMBL)
• RNA secondary structure prediction: If a multiple alignment is given by the user, the information on conservative positions in it and compensation exchanges in some of those will be used - stems, including such positions, are given more chances to be included into the resulting secondary structure. The algorithm is the following: first all of the possible ways of fitting together different pieces of the sequences are looked for. Then locally optimal secondary structures are built from the helices found. Lastly, the final system construction is done optimizing the model energy of the system (includes inputs from conservative and complementary pairs with corresponding coefficients). (Genebee)
• PSCAN server page: A program to play with protein threading. Allows one to align two sequences, find a match in the database through email (more reliable) or without email.
• RNA-mfold and DNA-mfold: Performs RNA and DNA secondary structure prediction using nearest neighbor thermodynamic rules. The mfold software uses what are called nearest neighbor energy rules. That is, free energies are assigned to loops rather than to base pairs. Documentation for the programs and more detail about how the structures are computed can be found here. (M. Zuker at Washington University)
• SoWhat: The SoWhat WWW server predicts distance constraints between amino acids in proteins from the amino acid sequence. It uses a neural network based method to predict contacts between C-alpha atoms from the amino acid sequence. (CBS Denmark)
   

• Pasteur Institute:
  • STRIDE: Protein secondary structure assignment from atomic coordinates
  • DSSP: Definition of secondary structure of proteins given a set of 3D coordinates
  • DSC: Discrimination of protein secondary structure class
  • PREDATOR: Protein secondary structure prediction from a single sequence or a set of sequences
  • environ: calculate accessible as well as buried surface area in protein structure
  • confmat: Side chain packing optimization on a given main chain template for protein

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  Other Software and Information Sources:

• The VSNS BioComputing Division offers educational services over the Internet in bioinformatics/biocomputing. They have offered award winning online courses in sequence analysis. The site includes a hypertext coursebook, covering topics such as pairwise sequence alignments, networking, and multiple alignment. You can also find a collection of online exercises, called ``Sequence Analysis with Distributed Resources'', and ``Biocomputing For Everyone'' and ``Biocomputing For Schools'' Websites.
• The Banbury Cross Site is a web page for benchmarking gene identification software. Banbury Cross is at the Centre National De La Recherche Scientifique. This Benchmark site is intended to be a forum for scientists working in the field of gene identification and anonymous genomic sequence annotation, with the goal of improving current methods in the context of very large (in particular) vertebrate genomic sequences.
• CBIL bioWidgets, at the University of Pennsylvania, is a collection of software libraries used for rapid development of graphical molecular biological applications. It includes:
  • bioWidgets for Java(tm), a toolkit of biology-specific user interface widgets useful for rapid application development in Java(tm)
  • bioTK, a toolkit of biology-specific user interface widgets useful for rapid application development in Tcl/Tk
  • RSVP, a PostScript tool which lets your printer do nucleic acid sequence analysis; it generates very nice color diagrams of the results.
• Human Genome Project Information at Oak Ridge National Laboratory contains many interesting and useful items about the U.S. Human Genome Project. They also have a more technical Research site.
• FAKtory: A software environment for DNA Sequencing is at the University of Arizona. It is a prototype software environment in support of DNA sequencing. The environment consists of
  1. their software library, FAK, for the core combinatorial problem of assembling fragments
  2. a Tcl/Tk based interface
  3. a software suite supporting a database of fragments and a processing pipeline that includes clipping, tagging, and vector removal modules.
  A key feature of FAKtory is that it is highly customizable: the structure of the fragment database, the processing pipeline, and the operation of each phase of the pipeline may be specified by the user.
• Computational Analysis and Annotation of Sequence Data. This is a tutorial by A. Baxevanis, M. Boguski, and B.F. Ouellette on how to use alignment programs and databases for sequence comparison. It is a review that will appear in the forthcoming book Genome Analysis: A Laboratory Manual (Bruce Birren, Eric Green, Phil Hieter, Sue Klapholz and Rick Myers, eds) to be published by Cold Spring Harbor Laboratory Press. The hypertext version of the review is linked to Medline records, software repositories, sequences, structures, and taxonomies via the Entrez system of the National Center for Biotechnology Information.