The isolate annotations include virus type, host, geographical location and experimentally tested antiviral resistance.
For each isolate, annotations provided by NCBI were merged with the BacProt annotations to find ORFs being present or absent between two strains by using BLAST (E value ≤ 10 − 4 ).
Both Java and PL/SQL are used to implement background algorithms such as isolate annotation and import/export of isolate records from/to GenBank.
The result of a search query can be exported as a pair of one Microsoft Excel file containing isolate annotation and one FASTA file containing nucleotide or protein sequences.
The isolate annotation includes virus type, host, geographical location, as well as other imported and generated data, e.g. putative enhanced pathogenicity and human adaptation, or antiviral resistance computed from protein sequences.
Here the 44607 cross-pathway inhibiting pairs from five model organisms were isolated if the pathway annotations of inhibitor provider and target in a pair were different.
For example, the presence of several high-quality peaks of an isotopic series at the same retention time that all unambiguously point towards a particular metabolite should result in a putative annotation that is given higher confidence than an annotation from an isolated noisy peak that could have been produced by any one of a number of metabolites.
We used the zebrafish genome as a reference for assessing the sequence divergence of the isolated transcripts and for transcript annotation and characterization.
As the annotation of the isolated fast evolving transcripts is difficult due to the lack of sequence similarity with distant reference species, we are unable for the moment to assess the proportion of fast evolving non-coding RNAs in our dataset.
Moreover, a comparison of three genetically divergent G. intestinalis isolates allows improved annotation of protein coding genes and non-coding RNAs.
The Sc. pombe (isolate 972h-) genome, annotation and protein sequences were downloaded from PomBase [ 42] and RNA-seq reads [SRA: SRX040571] were downloaded from NCBI [ 43].
