Sentence examples for the representative sequences as from inspiring English sources
Alignments were retrieved for each of the representative sequences as described above.
Similarity searches with BLASTp [ 71] were done with the well-characterized protein domains contained in these representative sequences as queries against their respective domain of life.
The X-ray structures of the representative sequences were used throughout this study as representative structures for the corresponding GH family.
The outcomes of the BLAST searches using the representative sequences published for the 12 TEs as the queries revealed the total hit numbers, alignments of the hit sequences, and the bit scores.
The representative sequence clusters as described before were analyzed for the presence of conserved motifs upstream of their operon.
Most programs measure conservation by counting the sequences that the reference amino acid is conserved, but selecting only representative sequences as counting can be easily skewed by uneven representation of sequences from different species and contamination of databases.
The program (CD-HIT) takes a fasta format sequence database as input and produces a set of 'non-redundant' representative sequences as output by removing the highly similar sequences.
The HMMs were created using HMMER3, with manually adjusted alignments of representative sequences as seed.
When different isoforms of a protein are recorded in the RefSeq database, the longest sequence was selected as the representative sequence (RS) and the others were treated as related sequences.
We assigned the representative sequence from each cluster, as determined by cd-hit, to its relevant ADAR category.
Protein sequences encoded by the SSH transcripts or by the representative sequence of each probeset as provided by the NetAffx Analysis Center [ 70] were predicted using a consensus generated by three different CDS predictors [ 71].
