specificity transcriptome:
the transcriptome selected for specificity analysis
Entrez GeneID:
a gene which corresponds to the target transcript
siRNA guide strand:
a 21-nucleotide sequence fully complementary to
the targeted transcript
siRNA sense strand:
a 19-nucleotide sequence complementary to the nucleotides 1-19 of the siRNA guide strand, and extended by 2 dT 3'-overhangs
start:
the starting position of the siRNA guide strand relative to the input sequence
rank:
predicted-specific siRNAs are ranked first by Biopred score, followed by siRNAs with low complexity (as defined by DUST) and by non-specific siRNAs
Biopred score:
a score between 0 and 1 which reflects the predicted inhibitory activity of the siRNA
specificity:
1: a siRNA which has at least 2 non-contiguous, non-terminal missmatches|insertions|deletions and a l-hit <16 to all non-targeted transcripts within the selected transcriptome
-1: a siRNA as described above but which has a low complexity subsequence
0: a siRNA which has less than 2 non-contiguous, non-terminal missmatches|insertions|deletions or a l-hit >=16 to at least one non-targeted transcript within the selected transcriptome
l-hit:
the length in nucleotides of longest siRNA subsequence
perfectly matching to a non-targeted transcript
negative control guide strand:
a 21-nucleotide sequence which has 3 non-contiguous, non-terminal nucleotides mismatched with the target sequence and has at least two non-contiguous, non-terminal mismatches|insertions|deletions and a l-hit <16 to all transcripts of the selected transcriptome
negative control sense strand:
a 19-nucleotide sequence complementary to the nucleotides 1-19 of negative control guide strand and extended by 2 dT 3'-overhangs
