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Together with the reciprocal procedure, both preference values were used to calculate the performance index.
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Prokaryotic homologues were added to the clusters using a reciprocal BBH procedure applying an e-value threshold of ≤1 × 10−10 and ≥30% identical amino acids.
Genomes for which proteins were not found using the four-letter synonym were searched by reciprocal BBH procedure using an already identified protein from the same lineage (see below) as a query and the genome in question as subject.
The reciprocal BLASTp procedure for identifying orthologous groups among Dehalococcoides was also applied to Dehalogenimonas lykanthroporepellens BL-DC-9 in comparison to Dehalococcoides ANAS, KB-1, 195, DONNA2, CBDB1, BAV1, GT, and VS; resulting in 432 core orthologous groups that were also free of paralogs.
In order to enable this type of genome content normalization, we used the same 31 Pfam profiles and the reciprocal search procedure to determine the number of genes belonging to our detoxification set in 835 fully sequenced and annotated bacterial genomes (Additional file 3).
Reciprocal function.
The intervention comprised the alternate use of L1 (Mandarin) and L2 (English) reciprocal teaching procedures.
Its methods have been described in detail, including the reciprocal inflation procedures used to generate national estimates from the sample [17, 18].
As soon as the 8.4x annotated grapevine genome sequence was available [ 1, 32], its annotation was used to confirm its true orthologous relationship by a reciprocal best match procedure as described in [ 1].
For achieving this, two reciprocal suppressive/subtractive hybridization procedures (SSH) were applied to early (11 weeks) human placental villi after incubation either in normoxic or in hypoxic conditions.
Two rice cultivars, Takanari and Koshihikari, developed in Japan, were used to develop the reciprocal CSSLs using the procedure summarized in Figure 2.
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