Sequences

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• Sequence alignment

• Sequence format conversion

• Sequence manipulation

• Sequence analysis

• Sequence assembly

• Sequence retrieval

• Sequence search

• Sequence annotation

• Major sequence databases

• ClustalX

• Sequence databases

[edit] Sequences - Web Resources

Entrez Gene includes records from fully sequenced genomes. Data available includes nomenclature, map location, gene products, markers, phenotypes, citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. Data is sourced from both curation and automated integration of data from RefSeq, from collaborating model organism databases and from other databases within NCBI. Records have unique identifiers, in the form of stable and tracked integers.

RefSeq NCBI reference sequences is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. In 2006, the database included 3774 organisms spanning prokaryotes, eukaryotes and viruses, and has records for 2 879 860 proteins. RefSeq records integrate data about a sequence and its features from many sources, with input from the scientific community, prediction, propagation from GenBank and curation by NCBI staff. Annotations include coding regions, conserved domains, tRNAs, sequence tagged sites (STS), variation, references, gene and protein product names, and database cross-references. RefSeq is quality controlled.

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ClustalW
Standard alignment tool. Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation.