A: Per analysis, PseudoChecker allows to test one candidate gene and imposes no limit to the number of target species, with one reference species.
A: PseudoChecker allows up to 10 MB of information per input of biological sequence set (genomic sequence per target species, coding exons and CDS of the reference species' in-study candidate gene and predetermined coding sequences).
A: PseudoChecker should be capable of handling several genes in a given target species' genomic sequence. However, if this contains highly similar, paralogous genes to the viable or inactivated orthologous counterpart of the in-study gene, this might interfere with the coding sequence prediction of it in the same species. For this reason, per target species, the user is advised to input the smallest possible genomic portion underlying a viable or inactivated version of the in-analysis gene.
A: PseudoChecker is capable of incorporating into a given analysis all types of genomic sequences, regardless of their fragmentation status and/or gap content and origin in terms of sequencing techniques. Nonetheless, since alignments of each reference exon against each test species' genomic sequence are conducted during the 1st component of the pipeline, incomplete or gapped sequences may hinder the in-study gene's orthologous exons prediction, putatively making a false inference regarding exon loss. For this reason, per target species, the user is advised to, whenever possible, include a genomic sequence fully underlying a viable or inactivated version of the in-study gene, simultaneously containing the fewest possible number of gaps.
A: Per analysis, PseudoChecker incorporates a single gene isoform. To this effect, we advise the user to individually test all annotated isoforms for the candidate gene of interest, so all possible scenarios associated with isoform loss/functionality are addressed with the software.
A: Yes. Even though these do not constitute the core of PseudoChecker 's purpose, this software displays two additional functions:
1. It can be used for comparing reference exons and CDS against single or multiple cDNA molecules, simply by replacing the main purpose genomic input sequences for target cDNA sequences: this being particularly useful for detecting sings of gene erosion within transcripts;
2. It can be used for comparing a reference cDNA molecule against single or multiple cDNA molecules, simply by replacing the main purpose genomic input sequences for target cDNA sequences and the reference species' exons and CDS for a simulated single-exon gene corresponding to the reference cDNA molecule itself.
A: If you need additional help, please feel free to contact us by sending an e-mail to luis.alves@ciimar.up.pt.