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There are no repeating or overlapping sequences in either genomic sequences, suggesting SjIR-1 and 2 are single copy genes in S. japonicum.
We took advantage of these intrinsic Pro-Gly residues and mutated the 2 upstream and downstream residues to cysteines to generate three DAT constructs with CCPGCC sequences in either extracellular loops 2, 3 or 4 (termed DAT EL2-CCPGCC, EL3-CCPGCC and EL4-CCPGCC, respectively).
The unmapped sequences were BLASTed against the genome and EST, and hairpin RNA structures encompassing sequ-seqs were predicated from the adjacent 60 nt sequences in either direction complying with criteria from the statistics of mammalian pre-miRNAs in miRBbase 13.0 using UNAfold software [51].
In analysis mode, D-Tailor reads a set of sequences in either delimiter separated (e.g. CSV) or FASTA format files.
Those targets that were extended into the regions without reference sequences (shown as 'N's in the genome reference sequences) in either genome were discarded.
The cucumber RGH query sequence and that of melon hits were considered orthologs when the sequence identify was >90%, the coverage was >95%, and no paralogous sequences in either genome.
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The 30 annotated sequences encode DREB transcription factors (9 sequences), proline dehydrogenases (2 sequences), sucrose synthases (4 sequences), and sequences involved in either gibberellin or glutamate biosynthesis (6 and 7 sequences, respectively).
Not surprisingly, there were almost no telomeric-related repetitive sequences or rDNA sequences identified in either potato or tomato BAC sequences.
We extracted the inverted human sequence and 1 kb of flanking sequence in either direction of the inversion.
For GC content analysis, 10 kb of flanking sequence in either direction of each RRMI locus was collected.
After obtaining the human and chimpanzee genomic positions for each inversion locus, we extracted 15 kb of flanking sequence in either direction of the human genomic position.
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