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Homepage-Tools

Bioinformatic links

NCBI (databases, PubMed, blast)
ReadSeq, SeqVerter, DNA Duster (Sequence format conversion and edition)
Reverse Complement, Reverse Complement, Batch Reverse Complement (Reverse Complement)
BioWiki
BioForum
Ensembl
bioinfo/molbio forum
Invitrogen Vector NTI Advance 10.3 - all in 1 Software - free for non-profit/ academic users

Standard List for AFLP Primer Nomenclature
Codon Usage Database
Exonerate - tool for CDS prediction - (Slater, G.S. and Birney, E. 2005. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6: 31.)
Tools zu Sequenzvergleichen am EBI (sequence analysis)
bioinformatic course Universität Halle-Wittenberg by Dr. Ralf Koebnik
toolz in web
toolz download
viele Toolz für Linux
viele toolz
Gene Identification - viele links
tools and links (1, 2, 3, 4, 5, 6, 7)
many molecular tools
toolz at Viral Bioinformatics Ressource Centre
nucleic acid database - a repository of three-dimensional structural information about nucleic acids
Transcriptional Regulatory Regions
MOBS
PRESTA - Promoter database
TaqMan SNP Assay
SNPs - Presentation
DCODE.org - Comparative Genome Centre

Xenomics - Xenopus tropicalis computational resources
Insitu.dcode.org - Xenopus tropicalis in situ database
Reverse complement a nucleotide sequence
Primers/oligos selection tool
Batch sequence retrieval from the UCSC Genome Browser

Restriction-Analysis
NEBcutter 2.0
REBASE - The Restriction Enzyme Database

Alignments
A more recent study of multiple alignment methods, with some excellent descriptions of the ten they tested, is found in this paper:
Nuin et al., 2006, BMC Bioinformatics --> Highly recommended. Interestingly T-COFFEE still does very well, although the best methods are some of the most recent, MAFFT and ProbCons.

• CLUSTAL W 1.83 (Higgins et al. 1994)
• MUSCLE (Edgar 2004)
• EMBOSS pairwise Alignments (Smith & Waterman 1981)
• Invitrogen Vector_NTI Software v10
• Multiple sequence alignment based on Fast Fourier Transform (MAFFT) (Katoh et al. 2005)
• T-COFFEE
• ProbCons


• eShadow - Phylogenetic shadowing of closely related species.
• zPicture - Stacked pairwise and multiple sequence alignment.
• MULAN - Full multiple sequence alignment. [Interactive conservation profiles, phylogenetic trees, etc.]
• ECR Browser - Evolutionary conservation of multiple genomes. Identification and sequence analysis of regulatory elements. Align your FASTA nucleotide sequence to a genome of choice.
• Splign - tool for computing cDNA-to-Genonomic, or spliced sequence alignments - 2004
• SLAM Web server for comparative gene finding and alignment
• Align-m Algorithm for multiple alignment of highly divergent sequences
• CLOURE Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics
According to "Lassmann T, Sonnhammer ELL, FEBS LETTERS 529 (1): 126-130 OCT 2 2002"
• DIALIGN (online) is better for more distant sequences, T-COFFEE (now with addition of 3D-COFFEE) for closer sequences. However they only looked at four methods. People suggest MUSCLE is very good also...
• DrawSeq Multiple sequence alignment graphics tool output as gif, pdf or postscript.
• Chroma CHROMA is a tool for generating annotated multiple sequence alignments in a convenient format for publication
• CorreLogo - 3D sequence logos of RNA and DNA alignments Generates 3D representation of alignment in VRML format and JavaView JVX format
• Base-by-Base - tool to visualize your multiple alignments etc...
• QAlign - Multiple alignment and editor using DCA, CLUSTAL-W, T-COFFEE, and DIALIGN (DOS Program working with commands)
• MGAlignIt - Web service for the alignment of mRNA/EST and genomic sequences (Multi)PipMaker
• SIM4
• FLAG
• Pfam
• Wise2 - Align a protein or profile HMM against genomic sequence to predict a gene structure, and related tools.
• MAVID

Sequence-attributes
• Tandem Repeats Finder (TRF) (Benson 1999)
• Cis-Element Cluster Finder (CISTER) (Frith et al. 2001)
• TFSEARCH - Searching Transcription Factor Binding Sites v1.3 (Akiyama et al.1998, Heinemeyer et al. 1998, Transfac matrix table rel. 3.3 (1998), taxonomic group: arthropod, threshold 85.0)
• TransFAC (Wingender et al. 2000)
• SynoR - Prediction of synonymous regulatory elements in vertebrate genomes.
• Creme 2.0 - Identification of cTFBS modules specific to promoters of co-expressed human genes.

Identification of conserved transcription factor binding sites (cTFBS) - Excluding up to 95% false positive TFBS predictions using sequence conservation as a filter.
• multiTF - cTFBS in multiple sequence alignments.
• rVista 2.0 - cTFBS in pairwise alignments.

tandem repeat search tools
http://tandem.bu.edu/trf/trf.submit.options.html (Tandem Repeat Finder 4.0)
http://c3.biomath.mssm.edu/trf.html
http://bioinfo.lifl.fr/mreps
http://strand.imb.ac.ru/swan/index.html
http://www.biophp.org/minitools/microsatellite_repeats_finder/demo.php
http://bioinf.dms.med.uniroma1.it/JSTRING/

search for TF binding sites in promotor regions
genomatix.de
Tfsitescan
signalscan
transfac
rvista.dcode.org
genomebiology.com

Primer design
alkami.com
premierbiosoft.com (free demo)
PrimerDesign
Primer 3 - empfehlenswert
!! PCR and Primer Design Links

Promoter predictions
• Promoter v2.0 prediction server (Knudsen 1999)
• Promoser v3.0 (Anason et al. 2003)
• Neural network promoter prediction (NNPP v2.2 1999) (Reese 2001)
• GENSCAN (Burge et al. 1998)
• FGENESH v2.5 (prediction of potential genes in honeybee genomic DNA)
• Dragon Promoter Finder v1.5 (Bajic & Brusic 2003)
• FPROM

• http://molbiol-tools.ca/Promoters.htm
• http://www.epd.isb-sib.ch/seq_download.html (The Eukaryotic Promoter Database)
• http://research.i2r.a-star.edu.sg/promoter/promoter1_5/DPF.htm
• http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=promoter

algorithms for detection of overrepresented motifs in two unaligned sets of UCR (upstream control region) sequences for specifically expressed genes (Cristino et al. 2006 - Ins. Mol. Biology)
AlignACE (Roth et al. 1998)
MEME (Bailey & Elkan 1995)
MDscan (Liu et al. 2002)

Software
Invitrogen Vector NTI Advance 10.3 - all in 1 Software - free for non-profit/ academic users
R - software for statistical modelling (introduction PDF)
fieldgenetics.com - parentage analysis program Cervus
Bayesian Analysis of genetic Population Structure (BAPS)
SAGA (download)
Lobster (download) (user guide) - Protein sequence analysis software
Prefab 4.0 (posted march 2005) database (download)
- PREFAB Protein Reference Alignment Benchmark - PREFAB is a database designed for testing multiple sequence alignment methods.
- Reference: Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.
Scoring software qscore
- scoring program that compares two multiple sequence alignments: an alignment to be evaluated (the "test" alignment) and a second alignment that is believed to be correct (the "reference" alignment). The program outputs the following scores:
- The PREFAB Q score (aka the Balibase SPS score or the Developer score).
- The Modeler score
- The Cline et al. shift score
- The Balibase TC (total column) score
viewer software JEvTrace
Programmdownloads (1, 2, 3)

Suppliers
Biomol
Fermentek
Quiagen
Sigma-Aldrich
Eppendorf
Applied Biosystems
Biometra

div. Links (noch nicht getestet)
Match 1.0 - Transcription Factor Binding Site Programs (designed for searching potential binding sites for transcription factors (TF binding sites) in any sequence of your interest)
SiteScan - Programs for Recognition TF binding sites: (E2F,...)
CompelScan - Programs for Recognition of Composite elements (NFAT/AP-1,...)
CompelPatternSearch 1.0 - program for searching potential composite elements similar to the COMPEL collection
SIGNAL SCAN is designed to analyze DNA sequences for transcription factor binding sites - most database formats accepted - IBM PC and Unix compatible versions
PatSearch - access only the TRANSFAC database - too many false positives found (mismatches allowed)
TESS - string-based and matrix-based searches (no more accessible? (tried 20/03/2001)
AliBaba2 - prediction of transcription factor binding sites by context dependent matrices generated from TRANSFAC 3.5 public sites.
MATRIXSEARCH/SIGNAL SCAN 4: FTP : beagle.colorado.edu, pub directory (imd.tar) - UNIX and IBM PC compatible versions, accepts Fasta or Staden sequence formats, but has its own precompiled database (IMD)
MatInspector (2) - a tool for detection of transcription factor binding sites. Macintosh, DOS, Windows 95 and NT, and UNIX compatible versions Accepts Staden, Fasta, IG, EMBL, GCG, or GCG-RSF sequence formats
ConsInspector (2) - related to MatInspector, also analyzes sequences surrounding the binding site VMS, UNIX, DOS, Windows 95, and Macintosh compatible versions
FunSiteP: Programs for Recognition Eukaryotic Pol II promoters
Grail - Exon prediction, polyAdenylation sites, simple repeats and CpG islands and more. UNIX compatible version
Promoter 2.0 Prediction Server - program for predicting vertebrate PolII promoters in DNA sequences. It has been developed as an evolution of simulated transcription factors that interact with sequences in promoter regions.
Promoter Prediction by Neural Network (NNPP version 2.2) - program for predicting vertebrate PolII promoters in DNA sequences. It was trained specifically to predict transcription startsites using sequence information from the core promoter region.
PROMOTER SCAN II (2)- program developed to recognize and predict polII promoters in genomic DNA sequences
Gene Finder - Splice sites, Protein coding exons and Gene models construction, Promotor and poly-A search.
Predicting Promoter Regulation and Recognizing Specific Types of Promoters - Staden Package of sequence analysis program
GenomeInspector - UNIX X Windows compatible version: FTP : ariane.gsf.de, pub/unix/genomeinspector directory
ModelInspector - with ModelGenerator - only one model (LTR) included, UNIX compatible version
PROMOTER SCAN II (2)

Alignment toolz @ http://pbil.univ-lyon1.fr/alignment.html:

Sequence Databases Retrieval Systems ( Genbank, EMBL, DDBJ, SWISS-PROT, TrEMBL, PIR, etc.) Search for sequence similarities in databases Web Sites for Pairwise Alignments Web Sites for Multiple Alignments Software for Multiple Alignments(download and install multiple alignment programs on your local computer) Multiple alignment editors
  • Jalview Java multiple alignment editor.(Java)
    Colour by amino acid physico-chemical property, similarity to consensus sequence, hydrophobicity or secondary structure. Gaps can be inserted/deleted using the mouse. UPGMA and NJ trees calculated and drawn based on percent identity distances. And much more ...
  • CINEMA 2.1 Colour INteractive Editor for Multiple Alignments (Java).
    Alignments may be loaded from the PRINTS fingerprint database. And much more ...
  • JavaShade Java multiple alignment editor. (Java)
  • SEAVIEW (For Mac, PC, Unix and Linux computers).
    A colour graphical interface to manually edit the alignment, and also to run dot-plot or Clustal W programs to locally improve the alignment. And much more ... Can be used in in combination with PHYLO_WIN for phylogenetic analyses.
  • MPSA (For Mac and Unix).
    Colour multiple alignment editor for secondary structure prediction.
  • Belvu (For Unix).
    Colour multiple alignment editor.
  • Se-Al (For Mac).
    Particularly useful for manipulating protein coding DNA/RNA sequences.
  • DCSE (For Unix).
  • STRAP (Java)
    Interactive extendable and scriptable editor for large protein alignments.
  • GoCore (Microsoft Excel)
    Open source "Microsoft Excel"-based bioinformatics tool for protein sequence alignment and analysis.
  • Kalignvu (Web-based multiple alignment viewer)
Pretty printing, shading, logos, etc. Databases of alignments Protein families.
  • PIRALN section of the Protein Alignment Database ( PIR)
  • HOVERGEN Homologous vertebrate genes (alignments and phylogenetic trees).
  • PROTOMAP hierarchical classification of all SWISS-PROT proteins.
  • Megaclass Molecular Sequence Megaclassification.

Protein domains.
RNA/DNA. Miscellaneous
  • PROTAL2DNA (Pasteur, Paris) Back-translate a protein alignment into a DNA alignment
  • JEvTrace (San Francisco, USA) Performs the Evolutionary Trace along with other phylogenomic analysis - it combines alignment, phylogeny and protein structure.
  • Mumsa (Stockholm, Sweden) A program to assess the quality of multiple sequence alignments
See also ... Index of services in molecular biology

Journals
Springer Journals
Springer Content Search
Springer - Insectes Sociaux
Springer - Arthropod-Plant Interactions
Springer - Behavioral Ecology and Sociobiology
BioControl
Biodiversity and Conservation
Biologia
Biological Invasions
Biology Bulletin
Chemoecology
Chromosoma
Chromosome Research
Conservation Genetics
Development Genes and Evolution
Ecosystems
Entomological Review
Evolutionary Ecology
Genetica
Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology
Journal of Insect Behavior
Journal of Insect Conservation
Journal of Mammalian Evolution (Content)
Journal of Molecular Evolution (Content)
Journal of Ornithology (Content)
Journal of Structural and Functional Genomics (Content)
Mammalian Genome (Content)
Molecular Biology (Content)
Molecular Diversity (Content)
Molecular Genetics and Genomics (Content)
Naturwissenschaften (Content)
Oecologia (Content)
Plant Systematics and Evolution (Content)
Population Ecology (Content)
Russian Journal of Ecology
Blackwell Synergy: Systematic Entomology
ZOOTAXA - A rapid international journal for animal taxonomists
PSYCHE - Journal of entomology
Directory of Open Source Journals

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© by Eckart Stolle 2006, www.tanemahuta.com/ek
mail: eckart.stolle(at)gmx.de