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Atlantic salmon BAC sequences surrounding the hemoglobin gene clusters were annotated using our in-house annotation pipeline described above.
Poly(A) clusters were annotated using the latest Arabidopsis genome annotation (TAIR10).
Aflatoxin gene clusters were annotated using MAKER (Cantarel et al. 2008) genome annotation pipeline and multiple alignments were performed using CLUSTALW (Thompson et al. 1994) and MUMMER (Delcher et al. 2002).
Clusters were annotated based on best hit against Swiss-Prot protein database [105] of members of that cluster (e-value <10−20 using BLASTP), or Pfam motifs contained in proteins from the cluster in the absence of Swiss-Prot hits.
Clusters were annotated using Blast2GO.
Finally, the clusters were annotated by manual curation.
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The clusters are annotated using sequence, structure and function descriptions based on the corresponding properties of its member fragments.
At the level of sequence and structure, the clusters
A total of 16 767 mouse transcript clusters are annotated to a RefSeq transcript.
Note that many of these clusters are annotated with broad terms such as "Signal peptide" or "Transmembrane".
The high degree of overlapping among GO terms can be best detected when we again determine the GO terms to which the proteins in the clusters are annotated.
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