MAGPIE A Java-based comprehensive project that studies the DNA properties and protein sequences
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protein study dna protein sequence study DNA DNA presentation

MAGPIE Description

A Java-based comprehensive project that studies the DNA properties and protein sequences MAGPIE or the Multi-purpose Automated Genome Project Investigation Environment is a software bundle for the automated presentation of DNA and protein sequences.In MAGPIE information about the coding likelihood of an ORF is shown as a set of 6 attributes. This information is provided in the contig graphics and in the ORF information line on the green page. The first three attributes fac reflect calculable properties of the sequence, whereas pdm describes how much external evidence (through database searches) we have about the sequence's function. The more blue (level 1) in the box, the more likely the ORF is really a coding sequence. ·F: (yes/no) Does the potential coding sequence fit this organism's codon usage profile (using a 99% confidence chi-square goodness of fit test) ·A: (yes/no) Is the A+G% of the sequence > 50%, characteristic of coding sequence in many organisms ·C: (level 1, 2, 3 or 4) What is the level of G+C compensation in the second and third codon positions? Most organisms will follow a pattern on G+C content being higher in the third 'waggle' position. ·P: (level 1,2 or 3) Indicates the best level of evidence we have that consists of a protein-level match (e.g. against GenPept, or protein-level mRNA/cDNA hit. ·D: (level 1, 2 or 3) Indicates the best level of evidence we have that consists of matches to DNA sequences at the DNA level of comparison (e.g. search against GenBank) ·M: (level 1, 2 or 3) Indicates the best level of evidence we have that consists of matches to protein families (e.g. PFam) or known binding site patterns (Prosite) Requirements: · Java

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