Finally, we included all 20,307 B. schlosseri predicted proteins with at least one intron and with RNA-Seq transcript support for at least 30% of the protein sequence.
To support the SignalP result, the protein sequences with predicted secretory signal peptides were also examined using iPSORT http://hc.ims.u-tokyo.ac.jp/iPSORT/.
Therefore, the protein sequences support the topology of Figure 1C as the most likely one for the relationship among the four mitochondrial lineages.
The best supported annotations, that agreed across two or more datasets, were presented along with supporting experimental and protein sequence evidence.
On the one hand, prediction of AS based on transcript sequence data seems to be overestimated in several filamentous fungi as cDNA-derived sequence data without supporting protein sequence data do not allow discrimination between AS and unprocessed or partially processed transcripts.
They are fully or partially supported by protein sequence records from several model organisms (XM-, XR- accession numbers).
For each alternative, the major variant was defined as the one supported by a protein sequence and having higher EST coverage.
We required that at least one path forming an alternative was supported by a protein sequence.
Basic and complex functionalities are both supported, such as protein sequence digestion, sequence feature predictions, file format readers and converters, spectrum preprocessing and peptide/protein post-processing, among others.
Codon-optimized PG9 heavy and light chain cDNAs (GeneArt, Regensburg, Germany; see Table S1 in Supporting information for protein sequences) were cloned with or without a C-terminal KDEL tag into the BsaI sites of pICHα31160 and pICHα26033, respectively.
