PseudoChecker consists in an integrated computational pipeline able to infer the coding status of a given eukaryotic nuclear protein-coding gene in single or multiple species of interest by taking advantage of existent genomic data.
(Genomic scaffold, genomic contig, genomic sequencing read - FASTA format)
(Exons should be inserted from the 5' to the 3' end of the gene - FASTA format)
(Match: 1; Mismatch: -3; Gap opening: -8; Gap extension: -1)
(Match: 1; Mismatch: -1; Gap opening: -8; Gap extension: -1)
Automatically chooses the similarity scoring scheme most adequate to each exon alignment
Minimum alignment identity between the reference species' coding exon and target species' genomic sequence to be considered as a valid alignment (30% minimum).
Frameshift cost Cost of an internal frameshift (those between the first and last codon)
Terminal frameshift cost Cost of a terminal frameshift (those in the first and last codon)
STOP codon cost Cost of a stop codon arising from the first to the penultimate codon
Gap opening Cost of internal gap opening (those between the first and last codon)
Gap extension Cost of internal gap extension (between the first and last codon)
Terminal gap opening Cost of terminal gap op. (before the first nt and after the last one)
Terminal gap extension Cost of terminal gap ext. (before the first nt and after the last one)
(Optional - FASTA format)