Bioinformatics for DNA Sequence Analysis.pdf - Index of

Similarity Searching Using BLAST 3Fig. 1.1. Growth of GenBank and DDBJ genetic databases over the past 10 years. TheINSDC databases have grown, over the past 10 years, approximately 168-fold in totalnumber of base pairs. While in the past the number of entries in INSDC databasesdoubled approximately every 2 years, a simple second-order polynomial regression(R 2 ¼0.9995) of the data over the past 10 years indicates that the next redoubling willtake a little over 4 years. This graph does not include HTG data.2. Program Usage2.1. Database FileFormatsOne of the largest sources of diversity among DNA databases liesin their file formats. While great efforts have been made to standardizefile formats, the various types and purposes of sequenceinformation and annotation entreat customized file types.2.1.1. FASTA Format First used with Pearson and Lipman’s FASTA program forsequence comparison (5), the FASTA file format is the simplestof the widely used formats available through the INSDC. It iscomposed of a definition or description line followed by thesequence. The definition line begins with a greater-than symbol(>) and marks the beginning of each new entry. The informationfollowing the greater-than symbol varies according to its source.Generally, an identifier follows (Table 1.1), after which optionaldescription words may be included. If the sequence is retrievedthrough NCBI’s databases, a GI number precedes the identifier.Though it is recommended that the definition line be no greaterthan 80 characters, various types and levels of information areoften included. The definition line is followed by the DNAsequence itself, in single or multi-line format. Nucleotides arerepresented by their standard IUB/IUPAC codes, includingambiguity codes (Table 1.2).