PanGEA: Identification of allele specific gene expression using the 454 technology

BMC Bioinformatics

Table 2 Performance of PanGEA-BlastN with the 454-platform using the recommended settings.

Values were calculated for mapping 1000 randomly excised ESTs, either to the genes or to the whole genome of D. melanogaster
¹ settings: word length 11; minimum diagonal 3; low complexity threshold 10; homopolymer Smith-Waterman algorithm; no maximum intron length
² length of the tags in bp
³ similarity of the tag with the target sequence in percent
⁴ ambiguous mapping results; min score difference for unambiguous best hit 12
⁵ correctly mapped tags (including ambiguous results containing the correct hit)
⁶ wrongly mapped tags (including ambiguous results not containing the correct hit)
⁷ no hit identified
⁸ number of long gaps (> 50 bp), putative introns
⁹ mapping time in seconds, without the time required for constructing the word hash-table
¹⁰ settings as above, only the maximum intron length was set to 5000 bp

ISSN: 1471-2105