A Pack of Molecular Analysis Tools

• DNA Analysis
• DNA/Peptide Sequence Comparisons
• Data Tables
• Database Sequence Search & Retrieval
• Oligonucleotide Analysis
• Motif Searches
• Peptide Sequence & Structure Analysis
• Ribosomal RNA Analysis
• Sequence Formatting & Submission to NCBI

• NEBcutter Restriction Analysis
  NEBcutter is an on-line tool for restriction mapping nucleotide sequences that also features identification of non-overlapping ORFs.
• Watcut Restriction Analysis
  Alternative restriction enzyme analysis.
• Reverse Complement
  Convert DNA sequence data to it's Reverse Complement.
• Raw Translation of DNA
  Translate DNA sequence in all 6 possible frames.
• Formatted DNA Sequence Translation
  There are two sites you can use. The preferred one is located at www.justbio.com. You will need to register yourself with this site before you can use this tool and you must use Internet Explorer V5.5 (or better) or Netscape V6 (or better). This facility allows translation of DNA sequence in one, or more frames. The output is formatted as free text amino acid sequence as well as DNA sequence plus the aligned translation. This utility is a useful and fast way to format your sequence following an Open Reading Frame analysis.
  The second site is located at www.expasy.org/tools/dna.html. The output requires more manual intervention with a word processor to make the sequence presentation acceptable
• Graphical Open Reading Frames Analysis at NIH
  Graphically identify ORFs within DNA sequence data.
• Identification of Prokaryotic Promoters
  A neural network based program to find possible transcription promoters. From the Berkley Drosophila Genome Project
• RepeatMasker
  Screens DNA sequences for interspersed repeats and low complexity DNA sequences. Multiple sequences may me submitted in FASTA format
• EINVERTED, PALINDROME and EQUICKTANDEM
  Find inverted and tandem repeats in sequence data.
• Codon usage table analysis
  This Java applet analyzes a codon usage table and lists the codons for each amino acid and their relative abundance. This way of presenting a codon usage table makes comparing two tables much easier than with the usual form of the Codon Usage Database.
• Graphical Codon Usage Analyser
  Differences in codon usage among organisms can lead to a variety of problems concerning heterologous gene expression. The GCUA tools display the codon bias in a graphical manner.

• FASTA Email Server Access
  Comparison of nucleotide or peptide sequences against entries in DNA or peptide databases.
  
  
• BLAST Sequence Comparisons (NIH)
  Compare sequence data with those in a database. Standard nucleotide-nucleotide BLAST (BlastN); Standard protein-protein BLAST (BlastP).
  
  
• Advanced BLAST2 Search Service at EMBL
  Advanced BLAST2 differs from BLAST1 in providing gapped alignments for your query sequences. In addition, a parser which allows an overview of the HSP hits aligned against your query sequence has been incorporated.
• CLUSTALW Multiple Alignment
  Fully featured multiple alignment of DNA and peptide sequences using the WWW ClustalW interface at the Human Genome Center at the Baylor College of Medicine.

• Nucleotide and Amino Acid symbols
  Tables of nucleotide and amino acid symbols as well as some other useful data. Sourced from Australian National Genomic Information Service (ANGIS).
• SPP-1 Bacteriophage DNA Markers
  Table of fragment sizes of EcoRI digested SPP-1 Bacteriophage DNA
• Properties of Amino Acids
  Table of Amino acid single letter codes and basic chemical properties

• NCBI Database Search and Sequence Retrieval
  Search Genbank, EMBL and other databases for DNA and Amino acid sequences.
• NCBI Entrez
  The National Centre for Biotechnology Information Search and Retrieval system that integrates information from databases at NCBI. These databases include nucleotide sequences, protein sequences, macromolecular structures, whole genomes, and MEDLINE, through PubMed.
• Other Searchable Databases
  A catalog of searchable databases grouped as genomic, nucleic acid, protein, organism specific and uncategorised.

• Primer 3: WWW primer tool
  Powerful PCR primer design program permitting one considerable control over the nature of the primers, including size of product desired, primer size and Tm range, and presence/absence of a 3’-GC clamp.
• PCR Suite
  Based on Primer 3, but has more stringent settings (to allow more working primersets) and a smaller range of
  parameters. The suite consists of four programs: Overlapping_Primers is for creating multiple overlapping PCR products in one sequence. Genomic_Primers designs primers around exons in genomic sequence. All you need is a GenBank file containing your gene. SNP_Primers designs primers around every SNP in a GenBank file. cDNA_Primers designs primers around open reading frames.
• GeneFisher: Interactive Primer Design
  Allows good control over primer design.
• Oligonucleotide primer selection
  Search for unique primers within a sequence
• Reverse translation tool
  This Java applet translates proteins into nucleotide sequences with adapted codon usage. This allows optimizing a sequence for expression in specific organisms
• Oligonucleotide Calculator
  Java Script Oligo calculator (Netscape V2 or better).

• Motif Search at ExPasy
  Search the Prosite database for functional motifs within peptide sequences.
• Search the BLAST Conserved Domain Database (rpsblast)
  Reverse Position Specific BLAST (RPS-BLAST) is a sensitive way of identifying conserved domains in proteins. The output of the analysis is in the form of conserved domain alignments. For additional information, refer to CDD help document. This analysis produces alignments with protein 3D structure. To view the 3D structures you will need the CN3D viewer. Read this file to get instructions on installing the viewer on a home Microsoft Windows system.

• Biotools
  Milton Saier's molecular analysis tools for peptide sequences.
• Transport Systems databases and analysis tools
  UCSD Transport System Databases, Phylogenetic analysis and related molecular analysis tools.
• Amino acid scale representation at ExPasy
  Hydrophobicity, other conformational parameters, etc.
• Prediction of Peptide Signal Sequences - SignalP or PSort
  Predict the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive and Gram-negative prokaryotes, and eukaryotes. Includes a PSort help manual.
• Protein Backtranslation Tool
  This Java applet translates proteins into nucleotide sequences with adapted codon usage. This allows optimisation of a sequence for expression in specific organisms. From Entelechon.com.
• Prediction of membrane-spanning regions (ISREC-Bioinformatics)
  TMpred program makes a prediction of membrane-spanning regions and their orientation.
• Swiss-Model
  An Automated Comparative Protein Modeling Server at ExPASy
• TMAP Membrane Protein Structure Prediction Service (EMBL)
  Prediction of Membrane Protein Structure for multiple aligned sequences. A service for single sequence input is also available is also available.
• Brookhaven Structure Database
  Simple Keyword search of the Brookhaven Structure Database. Retrieve X-ray crystallography cooordinates for display by RasMol. Rasmol for a variety of platforms can be obtained from ftp.dcs.ed.ac.uk/pub/rasmol/
• NCBI Molecular Modeling Database Service
  Entrez 3-D Structure Query of MMDB. Entrez/MMDB Structure FAQ page.
• Statistical Analysis of Protein Sequences (SAPS)
  This program, analyses proteins for statistically significant features like charge-clusters, repeats, hydrophobic regions, compositional domains etc. One of its options is to generate self-explanatory output.

• The RNA Fold Server
  A forms based WWW page to allow you to fold your own sequences on Zuker's Server. Your job can be processed while you wait (the default) or can be submitted for batch processing. If you select a batch job, make sure your E-mail address is correct. Current limits on job sizes are: Immediate job = 500 bases, Batch job = 2000 bases.

• Sequence Format Conversion
  Convert sequence data to any one of the accepted formats. Have a look at some example formats before you use this facility.
• Sequence Presentation Tool
  Overlay protein sequence data onto DNA sequence in publication style format.
• Bankit - Sequence Submission to Genbank by WWW
  BankIt allows you to use the World Wide Web (WWW) to submit sequences to GenBank. You can enter sequence information into a form, then revise it or add information about protein coding regions, mRNA features, and structural RNA features.
• WEBIN - Sequence Submission to EMBL/Genbank/DDJB by WWW
  WEBIN allows you to use the World Wide Web (WWW) to submit sequences to the International Databases in an easy and interactive way.