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Unigenes with BLAST results were mapped and annotated using the mapping and annotation functions of B2GO.
To assign gene ontology terms to each annotated sequence, successful blast hits were mapped and annotated using Blast2GO for the entire assembled transcriptome with the annotation cut-off threshold set to 55 and the GO level weighting set to 5. The single lane of Illumina HiSeq2000 produced close to 128 million paired-end reads (2 × 101 bp).
Sequence reads were mapped and annotated using Bowtie2 software [ 43].
Read statistics for the sequencing data when mapped and annotated to the sheep genome.
All blast hits were then mapped and annotated using the Blast2GO application with default settings for plants.
The ϕD5 genome was mapped and annotated using available phage genome sequences deposited in GenBank (http://www.ncbi.nlm.nih.gov/genbank/).nih.gov/genbank/
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Integration sites from published datasets [3], [19] were re-mapped and annotated according to the same criteria.
As a result, that part of the data (in, e.g., protein families) that has been thoroughly studied may possess a rich tree-structure whereas the rest is poorly mapped and weakly annotated.
The expression count data, cluster mapping, and annotated results.
The F. graminearum PH-1 strain was originally sequenced using Sanger technology, assembled into 433 contigs and 31 supercontigs, anchored to a genetic map, and annotated by the BROAD institute [ 4, 18].
The genes/proteins in each list were mapped, and then functionally annotated and searched for significant functional enrichment using the PANTHER pathways and biological processes categories.
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