DNA > Analysis   THE SMALL BIOINFORMATICIAN [PDF file, human molecular genetics rerefence data table]

REVIEW: Practical Database Searching   |   Bioinformatics.Org   |   ISCB   |   Pacific Symposia

Intro: Pedestrian guide to analysing sequence databases, by Rost and Schneider, 1999

Intro: USER'S GUIDE TO THE HUMAN GENOME - The NCBI Handbook

Intro: A Science Primer - at NCBI | Current Topics in Genetics Analysis at NIH VideoCasting

AIBG - Database and Bioinformatic Tools

Courses: Corso di Bioinformatica (Ita) - Bioinformatics Tutorials & Articles

Comments: Mining for Bioinformatics Jobs

Sequence Analysis Similarity - Align - Pattern - Express - Phylogen - Util - Protein

1) Initial similarity search

• Documents/Guides

• Blast Database Format
• BLAST TUTORIALS at NCBI - BLAST Tutorial - BLAST COURSE: The Statistics of Sequence Similarity Scores
• Sequence Analysis with distributed Resources - BLAST
• Primer BLAST Course
  
• NetBLAST educational at Weizmann
• WU-Blast2 server at the European Bioinformatics Institute (Lopez et al., 2003)
• Sequence comparison: basic concepts
• Protein Sequence Alignment and Database Scanning, by G. Barton
• WWW Tools
• BCM Search Launcher: Nucleic Acid Sequence Searches
• Swiss EMBnet node web server (Falquetet al., 2003)
• Protein machine Nucleotide to protein translation at EBI UK
• Smith-Waterman similarity search
• Diamond - alignment of sequencing reads against a protein reference database (Buchfink et al. 2015)
  

• BCM Search Launcher: Gene Feature Searches
• Computational Gene recognition:
• HMM-based
• Genie: A Gene Finder Based on Generalized Hidden Markov Models - Genie Web server
• Genscan at MIT - Identification of complete gene structures in genomic DNA
• HMMgene - Prediction of vertebrate and C. elegans genes
• GeneMark-HMM - Eukaryotic
• Combination of prediction and alignment
• Gnomon NCBI gene prediction tool - a combination of homology searching with ab initio modeling
  
• TWINSCAN
• Syntenic Gene Prediction Program SGP-1 - post-processing of two sequences to predict genes
• SLAM - submit pairs of syntenic sequences for gene annotation and alignment (Cawley et al., 2003)
• Others
• TIGR software: GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders (Majoros et al., 2003)
• AAT - Analysis and Annotation Tool for Finding Genes in Genomic Sequences
• FGENES - Splice sites, Protein coding exons at Sanger Centre
• Grail at ORNL - Gene Recognition and Assembly Internet Link - Version 1.3
• MZEF - Prediction of putative internal protein coding exons in genomic DNA sequences
• PROCRUSTES - Gene Recognition via Spliced Alignment
• WebGene - Tools for prediction and analysis of protein-coding gene structure
• PEDANT computational analysis of complete genome sequences (Riley et al., 2005) - PEDANT computational methods
• EUGENE'HOM - a generic similarity-based gene finder using multiple homologous sequences (Foissac et al., 2003)
• FirstEF - First-exon and promoter prediction program for human DNA
• ETOPE - evolutionary test of predicted exons (Nekrutenko et al., 2003)
• ESEfinder - a web resource to identify exonic splicing enhancers (Cartegni et al., 2003)
• GeneSeqer@QlantGDB - gene structure prediction in plant genomes (Schlueter et al., 2003)
• AGenDA - Alignment-based Gene Detection Algorithm (Taher et al., 2003)

• DNannotator - annotation software tool kit for regional genomic sequences (Liu et al., 2003)
• Bioverse - functional, structural and contextual annotation of proteins and proteomes (McDermott & Samudrala, 2003)
• FrameD - gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences (Schiex et al., 2003)
• AMIGene - Annotation of MIcrobial Genes (Bocs et al., 2003)
• AHMII - Agent to Help Microbial Information Integration (Sugawara & Miyazaki, 2003)
• Genescript Annotation Pipeline (program) (Hudek et al., 2003)
• GANESH: Software for Customized Annotation of Genome Regions (Huntley et al., 2003)

2) Alignment of Hits Similarity - Pattern - Express - Phylogen - Util - Protein

Pairwise Sequence comparison

• Documents/Guides
• Wiki List of Sequence Alignment Software
  
• Pairwise Sequence Alignment at BioComputing Hypertext Coursebook
• Sequence analysis with distributed resources: Pairwise sequence alignment
• Family Pairwise Search
• BCM Search Launcher: Pairwise Sequence Alignment

Next Generation Sequencing - Alignment

Multiple Sequence Alignments

• Documents/Guides
• A Gentle Guide to Multiple Alignment at BioComputing Hypertext Coursebook  |
• Sequence analysis with distributed resources : Multiple sequence alignment
• Algorithms for Multiple sequences alignment
• Protein Sequence Analysis au at Department of Biochemistry and Molecular Biology University College London
• C40 WWW PRACTICAL; a gentle introduction to global sequence and structure analysis facilities
• WWW Tools
• BCM Search Launcher: Multiple Sequence Alignments  |  CAP3 Sequence Assembly Program
• CLUSTALW interactive Muliple Sequence Alignment at EBI (Chenna et al., 2003)
• RevTraos - muluiple alignment of coding DNA from aligned amino acid sequences (Wernersson & Pedersen, 2003)
• MAVID - multiple alignment server (Bray & Pachter, 2003)
• Tcoffee@igs - computing, evaluating and combining multiple sequence alignments (Poirot et al., 2003)
• AMAS  |  JalView - Java alignment editor
• QAligo Home


• Genomic sequences
• Theatre - detailed comparative analysis and visualization of genomic sequence (Edwards et al., 2003)
• MultiPipMaker - alignments and analysis of multiple genomic DNA sequences (Schwartz et al., 2003)
• EnteriX 2003 - visualization tools for genome alignments of Enterobacteriaceae (Florea et al, 2003)

3) Derivation of a pattern Similarity , Align - Express - Phylogen - Util - Protein



• Documents/Guides
• Distant homologies: motifs, patterns, profiles - by Pongor and Vlahovicek, 1996
• Hidden Markov Models for Detecting Remote Protein Homologies
• Protein sequence and structure analysis: A practical guidef
• WWW Tools
• BCM Search Launcher: General Protein Sequence/Pattern Searches
• Species-Specific Protein Sequence Searches
• InterPro: search simultaneously: PFam+PRINTS+PROSITE+ProDom+SWISS-PROT+TrERMBL (Mulder et al., 2005)
• UniProt (Universal Protein Resource)
• SYSTERS Cluster Set (Meinel et al., 2005)
• Families: Additional Protein Family Sites
• Families: Browse families
• The PANTHER database of protein families, subfamilies, functions and pathways (Mi et al., 2005)
• FunShift: a database of function shift analysis on protein subfamilies (Abhiman and Sonnhammer, 2005)
• ProtoNet 4.0 - A hierarchical classification of one million protein sequences (Kaplan et al., 2004)
• SVM-Prot - functional family classification of a protein from its primary sequence (Cai et al., 2003)
• PipeAlign - a new toolkit for protein family analysis (Plewniak et al., 2003)
• *
• The definition of protein regions are mainly from: Bork & Gibson, 1996
• MOTIFS - Small conserved regions within larger entities
• Concept: restriction to key conserved features to reduce the higher "noise" level of the more variable regions
• Geneva's Expasy - PROSITE - Database of Protein Sites and Patterns (Hulo et al., 2004, 2006)
• ScanProsite - Scan a sequence against PROSITE or a pattern against SWISS-PROT
• Frame-tolerant profile scan
• SMART - Simple Modular Architecture Research Tool (Letunic et al., 2004, 2006)
• ELM server - investigating short functional sites in modular eukaryotic proteins (Puntervoll et al., 2003)
• ProDom   (BLAST search of ProDom) - Database of protein domains (Bru et al., 2005)
• The CATH Domain Structure Database, Gene3D, DHS - domain family information for genome analysis (Pearl et al., 2005)
• DOMO - searchable by SRS - (Delineation of domain boundaries from sequence similarities, in Bioinformatics)
• Pmotif finds protein motifs in DNA
• MEME - Introduction
• eBLOCKs - enumerating conserved protein blocks to achieve maximal sensitivity and specificity (Su et al., 2005)
• Identification of polymorphic motifs using probabilistic search algorithms (Basu et al. 2005) (MOTIFIND program: require)
• PSORT - Prediction of protein sorting signals (Gardy et al., 2003; Rey et al,, 2005)
• DBSubLoc: database of protein subcellular localization (Guo et al., 2004)
• Organelle DB - a cross-species database of protein localization and function (Wiwatwattana and Kumar, 2005)
• BPROMPT - a consensus server for membrane protein prediction (Taylor et al., 2003)
• THGS: a web-based database of Transmembrane Helices in Genome Sequences (Fernando et al., 2004)
• PDB_TM - selection and membrane localization of transmembrane proteins in the protein data bank (Tusnady et al., 2005)
• Signal search analysis server (Ambrosini et al., 2003)
• big-{Pi} - GPI Modification Site, NMT - Myristoylation  and PTS1 - peroxisomal signal predictions (Eisenhaber et al., 2003)
• SEARCHPKS - a program for detection and analysis of polyketide synthase domains (Yadav et al., 2003)
• SPEPLip - Predictor of Signal Peptide and Lipoprotein Cleavage Sites in Proteins
• SPD - a web-based secreted protein database  (Chen et al. 2005)
• *
• BLOCKS (aligment blocks) - conserved patterns of multiple alignments, containing no ins or del
• BLOCKS home page at Hutchinson, Seattle -
• Block Searcher to search a sequence vs Blocks;   Block Maker to create Blocks
• *
• PATTERNS - small motifs or larger regions containing several motifs; may contain gaps
• Pfam homepage at The Sanger Centre  (Search Pfam, also starting from DNA) - (Bateman et al., 2004, Finn et al., 2006)
• PIR superfamily/family classification (PIRSF) - (Wu et al., 2004)
• CDD - a Conserved Domain Database and Search Service at NCBI (Marchler-Bauer et al., 2005)
• DART - Domain Architecture Retrieval Tool (lists proteins with similar domain architectures)
• ADDA - a domain database with global coverage of the protein universe (Heger et al., 2005)
• SBASE web server (database of protein domains) at ICGEB, Ital (Vlahovicek et al., 2005)
• DDBASE (DIAL-derived domain database) - A database of Globular domains (Vinayagam et al., 2003)
• PatScan - pattern scanning
• IBM's Bioinformatics and Pattern Discovery group (Huynh et al., 2003)
• PatSearch - detection of patterns and structural motifs in nucleotide sequences (Grillo et al., 2003)
• Patterns in biological sequences at the ALGGEN server: PROMO and MALGEN (Farre et al., 2003)
• *
• PROFILES - full representation of features in aligned sequences (position-dep weight/penalties for all 20 AA, ins and del)
• Concept: including all possible information to maximize the overall signal of the entity (protein/domain)
• ProfileScan - Scan a sequence against the profile entries in PROSITE
• UCSC HMM Applications Main Page - SAM-T02 model library query
• The Sanger Centre : Genewise submission
• HMMER - profile hidden Markov models
• ORFeus - detection of distant homology using sequence profiles (Ginalski et al., 2003)
• The CAP Sequence Assembly Machine
• Probe README
• *
• FINGERPRINT - group of conserved motifs used to characterise a protein family.
• Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space.
• PRINTS (Attwood et al., 2000), at UMBER; search with SPRINT or P-val FingerPRINTScan
• AnaGram: protein function assignment based on protomotifs (Perez et al., 2004)
• *
• Software to download
• PROFILE: ftp.ebi.ac.uk/pub/software/unix/ [classical profilesearch]
• MoST [motif search tool]
• CAP [blastp output parser]
• *
• MOTIF/PROFILE BASED DATABASE SEARCH (return to 1)



4) Expression Analysis Similarity - Align - Pattern - Phylogen - Util - Protein

cDNA DATABASES

• dbEST - UniGene - cDNA relational Databases () (in Filemaker Pro)
• NCBI Reference Sequence (RefSeq) - curated non-redundant sequence database (Pruitt et al., 2005)
• H-Invitational Database (H-InvDB) (Imanishi et a., 2004)
• BCM Human Transcript Database Home Page | TIGR gene index (Lee et al., 2005)
• DBTSS: human transcr. start sites / full-length cDNAs (Suzuki et al., 2004)
• A comprehensive transcript index of the human genome (Schadt et al., 2004)
• A genome annotation-driven approach to cloning the human ORFeome (Collins et al., 2004)
• Full-lenght cDNA Projects   -   Human:
• Mammalian Gene Collection (MGC)   |   German (MIPS) (Mewes et al., 2004)
• HUGE (Kazusa) (Kikuno et al., 2004)   |   NEDO (Suzuki et al., 2004)
• Representative Transcript and Protein Sets (RTPS) (FANTOM2) full-length cDNA set (human, mouse, and rat)
• HUNT - Human Full Length cDNA Database
• Cancer Genome Anatomy Project (CGAP)   |   Understanding CGAP
• Cancer gene expression database (CGED) - gene expression profiling of human cancer tissues (Kato et al., 2005)
• SOURCE - Stanford Online Universal Resource for Clones and ESTs (SOURCE) compiled informations
• CaGE: Cardiac gene expression knowledgebase - paper on Bioinformatics, Jul 2002
• EST Projects: The I.M.A.G.E. Consortium - WashU-Merck   |   EST-PAGE (EST data entry) (Matukumalli et al., 2004)
• EST Traces: at NCBI; at WashU
• PolyA_D - a database for mammalian mRNA polyadenylation (Zhang et al., 2005)*ng et al., 2005)


• 
  

EST ASSEMBLING AND ALIGNING

• *The EST Machine at TIGEM   *EST Links at EBI
• *CAP3   *ESTBlast | est_genome   *UniBlast (Blast vs. human UniGene clusters)
• *BodyMap-Xs - anatomical breakdown of animal ESTs for cross-species comparison of gene expression (Ogasawara et al., 2006)
• *MVIEW: view Blast results as a multiple alignment (N. P. Brown)
• *SIM4 - cDNA and Genomic DNA alignment
• *MGAlignIt - alignment of mRNA/EST and genomic sequences (Lee et al., 2003)
• *ESTAnnotator - a tool for high throughput EST annotation (Hotz-Wagenblatt et al., 2003)
noncoding and antisense RNAs

• noncoding RNA database at Poznan, Poland
• RNAdb - a comprehensive mammalian noncoding RNA database (Pang wt al., 2005)
• NONCODE - an integrated knowledge database of non-coding RNAs (Liu et al., 2005)
• Rfam - annotating non-coding RNAs in complete genomes (Griffiths-Jones et al., 2005)
• The microRNA Registry at Sanger Institute - Griffiths-Jones, 2003
• *Antisensor - In silico detection of sense/antisense cluster pairs
• *AntiHunter - searching BLAST output for EST antisense transcripts (Lavorgna et al., 2004)

ALTERNATIVE SPLICING

• The Alternative Splicing Database (ASD) Project (Thanaraj et al., 2004; Stamm et al., 2006)
• HOLLYWOOD - a comparative relational database of alternative splicing (Holste et al., 2006)
• ASPic (Alternative Splicing Prediction) - gene exon-intron structure based on EST clusters (Bonizzoni et al., 2005)
• ASPicDB - alternative splicing analysis (Castrignano et al., 2008)


• 
  
• ECgene - genome annotation for alternative splicing (Kim et al., 2005; Kim et al., 2005b)
• RCDA [Windows command line] - sensitive and specific alternatively spliced transcript assembly (Sturgeon and Gardiner, 2012)


• SpliceInfo - an information repository for mRNA alternative splicing in human genome (Huang et al., 2005)
• ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome
• GeneFizz - compare genetic (coding/non-) and physical (helix/coil) segmentations of DNA (Yeramian & Jones, 2003)
• Alternative Splicing DB (ASDB) - Main Page
• Alternative Splice Finder - EASED: Extended Alternatively Spliced EST Database (Pospisil et al., 2004)
• SpliceNest: visualizing gene structure and alternative splicing based on EST clusters (Krause et al., 2002)
• Inferring Alternative Splicing Patterns in Mouse from a Full-Length cDNA Library and Microarray Data (Aug 2002 paper)
• ProSplicer - An Alternative Splicing Database based on Protein, mRNA, and EST Sequences - GenomeBiology March 14, 2003
• Gene and alternative splicing annotation with AIR (Florea et al., 2005) - tools (panther)
• Putative ALternative Splicing Database - PALS db
• ASAP II database - alternative splicing in 15 animal species (Kim et al., 2007)
• Fast-db - Human alternative splicing variants  (de la Grange et al., 2007)
• ASTD - The Alternative Splicing and Transcript Diversity database - (Koscielny et al., 2009)
• TassDB2 - TAndem Splice Site DataBase (database of subtle splicing)
• 
  
• SpliceAid2 - a database of human splicing factors
  


• 
  

SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs)

• SNP at NCBI |  BLAST SNP
• Leelab SNP Database  |  SNP at JST  |  GeneCanvas  |  SIMP (SNP Information Mining Pipeline)
• SNaP - SNP simulation
• FESD - a Functional Element SNPs Database in human (Kang et al., 2005)
• SNPeffect - molecular phenotypic effects of human non-synonymous coding SNPs (Reumers et al., 2005)
• PARSESNP - a tool for the analysis of nucleotide polymorphisms (Taylor & Greene, 2003)
• Pipeline Diversity Database
• Polymorphix - a sequence polymorphism database (Bazin et al., 2005)*


• 
  

EXPRESSION PROFILE

• Digital Differential Display (DDD) - human - Guide
• SAGE Digital Gene Expression Displayer (DGED) at CGAP
• GeneHub-GEPIS (Gene Expression Profiling In Silico) - gene expression patterns from integrated EST and tissue source information
• 5'SAGE - 5'-end Serial Analysis of Gene Expression database (Kasai et al., 2005)
• SAGE Gene to Tag Mapping
• MIRAGE (Molecular Informatics Resource for the Analysis of Gene Expression)
• DNA ARRAYS (in our "Methods" section)

5) Cross/species sequence comparison Similarity - Align - Pattern - Express - Util - Protein



• Documents
• The Mathematical Basis of Molecular Phylogenetics
• The Tree of Life Web Project  |  Taxonomy Browser at NCBI
• NEWT - a new taxonomy portal (Phan et al., 2003)
• Wikispecies  |  Species 2000 (Nature news, March 15, 2005)
• Curr Opin Genet Dev, 9:609-722, 1999 - (Genome Comparison)
• Tools
• DED - Database of Evolutionary Distances (Veeramachaneni and Makalowski, 2005)
• The Adaptive Evolution Database (TAED) - a phylogeny based tool for comparative genomics (Roth et al., 2005)
• Mulan - Multiple-sequence local alignment and visualization for studying function and evolution (Ovcharenko et al., 2005)
• Uprobe - A genome-wide universal probe resource for comparative physical mapping in vertebrates (Kellner et al., 2005)
• Prolinks - a database of protein functional linkages derived from coevolution (Bowers et al., 2004)
• Phylogeny Programs - Molphy  |  Paml  |  Passml  |  Puzzle  |
• Mac Software from Oxford Evolutionary Biology Group
• PAUP* 4.0
• CLUSTALW interactive Muliple Sequence Alignment at EBI - *BLAST+Phylogeny: EMBL
• PhyloBLAST - facilitating phylogenetic analysis of BLAST results
• TreeGen - constructs phylogenetic trees based on distance matrices
• PHYLIP Home Page
• Phylodendron
• ROSE - Random model of sequence evolution
• GeneOrder -  Comparisons of gene co-linearity in genomes
• GALA and dbERGE II - databases featuring genomic sequence alignment, annotation and experimental results (Elnitski et al., 2005)
• GRIMM -  Genome Rearrangements In Man and Mouse
• Phydbac (phylogenomic display of bacterial genes) - annotation of bacterial genomes (Enault et al., 2003)
• FootPrinter - a program designed for phylogenetic footprinting (Blanchette & Tompa, 2003)



*) Sequence utilities Similarity - Align - Pattern - Express - Phylogen - Protein



• BCM Search Launcher: Sequence Utilities - ReadSeq / Readseq at TIGEM / Readseq at BioWeb (Pasteur Institute)
• DNA analysis servers: plot.it, bend.it, model.it and IS (various DNA parameters) (Vlahovicek et al., 2003)
• RepeatMasker Web Server - RepeatMasker Documentation - MaskerAid
• SPA - simple web tool to assess statistical significance of DNA patterns (Richard & Nuel, 2003)
• Cluster-Buster - finding dense clusters of motifs in DNA sequences (Frith et al., 2003)
• SIC - a tool to detect short inverted segments in a biological sequence (Robelin et al., 2003)
• MAK - automated MITE (Miniature inverted repeat transposable elements) analysis (Yang & Hall, 2003)
• mreps - efficient and flexible detection of tandem repeats in DNA (Kolpakov et al., 2003)
• TRACTS - a program to map oligopurine.oligopyrimidine and other binary DNA tracts (Gal et al., 2003)
• The Sequence Manipulation Suite  |  Biology Workbench v3.2  |  Sequence Analysis at DeCypher   |   JaMBW
• Galaxy - web-based data analysis framework (Elnitski et al., 2005)
•  et al., 2005)Helmholtz Network for Bioinformatics (Crass et al., 2004)
• Translate at EBI
• SIRW - Simple Indexing and Retrieval System - sequence motif searches with keyword searches (Ramu et al., 2003)
• Standalone: BioEdit (Win) - All in One AiO: oligo, DNA and protein programs (Win)
• ALERT SERVICES
• Create & Send a Swiss-Shop Request



***

PROTEIN ANALYSIS

Protein primary structure analysis Similarity - Align - Pattern - Express- Phylogen - Util - Protein

• ExPASy - Proteomics Tools at ExPASy, Switzerland - proteomics server(Gasteiger et al., 2003)
• PARAMETERS CALCULATIONS
• ProtParam - Physico-chemical parameters of a protein sequence (amino-acid and atomic compositions, pI, extinction coefficient, etc.)
• Compute pI/Mw - Compute the theoretical pI and Mw from a SWISS-PROT or TrEMBL entry or for a user sequence
• MW, pI, Titration curve - Computes pI, composition and allows to see a titration curve
• REP - Searches a protein sequence for repeats
• SAPS - Statistical analysis of protein sequences at EMBnet-CH
• GlobPlot - exploring protein sequences for globularity and disorder (Linding et al., 2003)
• UniqueProt - creating representative protein sequence sets (Mika & Rost, 2003)
• COILED COIL AND PEST REGIONS PREDICTIONS
• Coils - Prediction of coiled coil regions in proteins (Lupas's method) at EMBnet-CH
• Paircoil- Prediction of coiled coil regions in proteins (Berger's method)
• Multicoil - Prediction of two- and three-stranded coiled coils
• ISREC COILS Server: prediction of coiled coil regions in proteins
• PESTfind - Identification of PEST regions at EMBnet Austria
• AMINO ACIDS GRAPHICS
• ProtScale - Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.)
• RbDe - building protein diagrams with the residue-based diagram editor (Skrabanek et al., 2003)
• Drawhca - Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence
• Protein Colourer - Tool for coloring your amino acid sequence
• Colorseq - Tool to highlight (in red) a selected set of residues in a protein sequence
• HelixWheel - Representation of a protein fragment as a helical wheel
• RandSeq - Random protein sequence generator - with options (e.g., amino acid composition)
• PROTEIN IDENTIFICATION
• TOOLS at Expasy server (calculations starting from experimental data about proteins)
• CRP - Cleavage of Radiolabeled Phosphoproteins (Mackey et al., 2003)
• JVirGel - calculation of virtual two-dimensional protein gels (Hiller et al., 2003)

Protein Secondary Structure Prediction Similarity - Align - Pattern - Express - Phylogen - Util - Protein

• Documents
• Secondary Structure Prediction methods and links
• JPred: a consensus secondary structure prediction server (Cuff et al., Bioinformatics, 1998)
• Comparison of methods (Geetha et al., Protein Eng, 1999)
• The principles of protein structure: a course using the Internet
• Tools
• BCM Search Launcher: Protein Secondary Structure Prediction
• Expasy: secondary structure prediction tools list
• EVA - evaluation of protein structure prediction servers (Koh et al., 2003)
• VADAR - a web server for quantitative evaluation of protein structure quality (Willard et al., 2003)
• Servers for sequence-structure relationship analysis and prediction (Dosztanyi et al, 2003)
• POPS - a fast algorithm for solvent accessible surface areas at atomic and residue level (Cavallo et al, 2003)
• NORSp - predictions of longregions without regular secondary structure (Liu & Rost, 2003)
• 3D-Jury - Structure Prediction Meta Server Input Page
• The PredictProtein server for protein structure prediction and sequence analysis (Columbia)   (Introduction) (Rost& Liu, 2003)
• JPred
• Protinfo - secondary and tertiary protein structure prediction
• GeneSilico - protein structure prediction meta-server (Kurowski & Bujnicki, 2003)
• META-PP - single interface to crucial prediction servers (Eyrich & Rost, 2003)
• Static benchmarking of membrane helix predictions (Kernytsky & Rost, 2003)
• Chou-Fasman Secondary Structure
• SSEP - secondary structural elements of proteins (Shanthi et al., 2003)
• DSSPcont - continuous assignment of secondary structure from PDB structures
• PSIpred: a protein structure prediction server
• FoReSST - FORESST: fold recognition from secondary structure predictions of proteins
• SCOP - structural classification of proteins (Andreeva et al., 2004 update)
• S4 - structure-based sequence alignments of SCOP superfamilies (Casbon and Saqi, 2005)
• JOY- protein structure and alignment analysis
• HOMSTRAD - Homologous Protein Structure Alignment Database (Stebbings & Mizuguchi, 2004 update)
• CAMPASS - CAMbridge database of Protein Alignments organised as Structural Superfamilies

Tertiary structure prediction and protein modelling

Similarity - Align - Pattern - Express - Phylogen - Util - Protein

• Levinthal's Paradox
• Course on protein structure and comparative modelling at ExPASy
• Corso di modeling (Esercitazioni di bioinformatica) at University of Padova (Ita)
• Homology modeling, model and software evaluation: three related resources (Rodriguez et al., Bioinformatics, 1998)
• Molecular Modeling of Proteins list of tools
• Biomolecular Modelling Home Page
• AlphaFold at EBI (Jumper et al., 2021)  - FAQ
  
• STING Millennium - comprehensive and simultaneous analysis of protein structure and sequence (Neshich et al., 2003)
• SWISS-MODEL - an automated protein homology-modeling server at ExPASy, Switzerland (Schwede et al., 2003; Kopp and Schwede, 2006)
• DINAMO - A Sequence Alignment Editor/Molecular Graphics Tool
• More about MATHMOL
• MATRAS - a program for protein 3D structure comparison (Kawabata, 2003)
• LGA - a method for finding 3D similarities in protein structures (Zemla, 2003)
• Tools for comparative protein structure modeling and analysis at Sali lab (Eswar et al., 2003)
• Databanks access and sequence/structure analysis services at the Pole Lyonnais - PBIL (Perriere et al., 2003)
• PFD (Protein Folding Database) - investigation of protein folding kinetics and stability (Fulton et al., 2005)
• *
• Mutation effects
• TRITON - a graphical tool for modelling protein mutants and assessment of their activities
• SIFT - predicting amino acid changes that affect protein function (Ng & Henikoff, 2003)
• Molecular Visualization Freeware - Protein Explorer, Chime & RasMol
• MolSurfer - a macromolecular interface navigator / protein-DNA/RNA interfaces (Gabdoulline et al., 2003)
• CASTp - Computed Atlas of Surface Topography of proteins (Binkowski et al., 2003)
• SEM (Symmetry Equivalent Molecules) - a web-based GUI to generate and visualize the macromolecules (Hussain et al, 2003)
• ESPript/ENDscript - extracting and rendering sequence and 3D information from atomic structures of proteins (Gouet et al, 2003)
• WebFEATURE - identifying and visualizing functional sites on macromolecular structures (PDB) (Liang et al., 2003)
• PDBSite - a database of the 3D structure of protein functional sites (Ivanisenko et al., 2005)
• 3MATRIX and 3MOTIF - a protein structure visualization system for conserved sequence motifs (Bennett et al, 2003)
• Motif3D - relating protein sequence motifs to 3D structure (Gaulton & Attwood, 2003)
• LOC3D - annotate sub-cellular localization for protein structures (Nair & Rost, 2003)
• Annotation in three dimensions. PINTS - Patterns in Non-homologous Tertiary Structures (Stark & Russell, 2003)

Protein interaction prediction

• ProteomeHD - Protein co-regulation analysis (Kustatscher et al., 2020)
  
• IPPRED - protein partners potentialy linked by an interaction relation
• NCI - a server to identify non-canonical interactions in protein structures (Madan Babu, 2003)
• MHCPred - a server for quantitative prediction of peptide-MHC binding (Guan et al., 2003)
• Scansite 2.0 - proteome-wide prediction of cell signaling interactions using short sequence motifs (Obenauer et al., 2003)
• iSPOT - infer the interaction specificity of families of protein modules (Brannetti & Helmer-Citterich, 2003)
• 3did - interacting protein domains of known three-dimensional structure (Stein et al., 2005)
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            Phenotype

• Phen-Gen - combines patients' disease symptoms and sequencing data (Javed et al., 2014)
  

Books

• Introduzione alla Bioinformatica - Zanichelli, 2003 (Ita)
Computational Biologists - some pages I found

• Altschul, Stephen F.
• Ashburner, Michael
• Barton, Geoffrey J. - secondary structure prediction, multiple alignment
• Birney, Ewan - Interview - sequence analysis, human genome annotation
• Boguski, Mark S.
• Bork, Peer
• Brenner, Steven E.
• Brownstein, Michael J.
• Casadio, Rita
• Doolittle, Russell F.
• Eddy, Sean R.
• Eisen, Michael B. - Lab
• Felsenstein, Joseph
• Gibson, Toby
• Gilbert, Walter - Intron evolution
• Gribskov, Michael
• Haussler, David
• Henikoff, Steven
• Hofmann, Kay
• Kanehisa, Minoru
• Koonin, Eugene V.
• Lake, James
• Makalowski, Wojciech
• Pearson, William R.
• Quackenbush, John - Whole Genome Functional Analysis at TIGR - Conference
• Rost, Burkhard
• Saccone, Cecilia
• Saitou, Naruya
• Staden, Rodger
• Stoeckert, Christian J - Gene expression databases and data analysis
• Thornton, Janet M.
• Trent, Jeffrey
• Young, Richard A. - Regulation of gene expression

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Last updated July 28, 2010

DNA