Nucleic Acid Analysis

Sequence Information

— Manipulation Tools

— Retrieval

— Similarity Searching

Manipulation Tools

• BIMAS ReadSeq
  Converts DNA or protein sequence input into various file formats
• CODON Usage Database
  Find the frequency of codon use in various organisms
• DNA Translator Tool Test
  Translate DNA to protein.
• EMBL-EBI BLAST2 EMVEC
  Check sequences for vector contamination. EMVEC is an extraction of sequences from the SYNthetic division of EMBL containing more than 2000 sequences commonly used in cloning and sequencing experiments
• EMBL-EBI GenMark
  Coding potential of DNA sequences
• EXPASY Translate Tool
  Allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence
• NCBI VecScreen
  Identify segments of a nucleic acid sequence that may be of vector origin
• Repeat Masker
  Screens DNA sequences for interspersed repeats and low complexity DNA sequences and returns a masked query sequence

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Retrieval

• DNA Data Bank of Japan (DDBJ)
  DDBJ is the sole DNA data bank in Japan and has been functioning as one of the International DNA Databases
• EMBL Nucleotide
  The EMBL Nucleotide Sequence Database constitutes Europe's primary nucleotide sequence resource
• NCBI dbEST: Database of Expressed Sequence Tags
  Database of expressed sequence tags; short, single pass read cDNA (mRNA) sequences. Also includes cDNA sequences from differential display experiments and RACE experiments
• NCBI Entrez Nucleotide
  Nucleotide sequences from >100,000 organisms in Genbank. Records that are annotated with coding region (CDS) features also include amino acid translations
• NCBI RefSeq
  Provides a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms

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Similarity Searching

• BCM Search Launcher
  Different alignment algorithms all on same site for pairwise sequence alignments, providing a single point of entry for: SIM,, BLAST 2, ALIGN, LALIGN, LAP 2, PGWISE, PCWISE
• BLOCKS
  Blocks are multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. Blocks Searcher, Get Blocks, and Block Maker detect and verify protein sequence homology to protein or DNA query sequences
• EMBL-EBI EMBOSS
  Compare two sequences either locally or globally
• EMBL-EBI FASTA
  Provides sequence similarity searching against nucleotide and protein databases using the Fasta programs
• EMBL-EBI Geneomes and Proteomes FASTA
  Sequence similarity searching against complete genomes databases using the Fasta programs
• MAP Multiple Sequence Alignment
  Uses the MAP program for alignment of multiple DNA or protein sequences
• NCBI MegaBLAST
  
• NCBI Nucleotide—Nucleotide (blastn)
  Find similar sequences to a query sequence from the Genbank nucleotide databases

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