BLAST analysis of the 62 clusters with a greater than two-fold difference in expression in the iL3 stage, compared with the L1 stage, shows that nine have no significant alignment, 25 have a significant alignment to known C. elegans proteins and 17 have a significant alignment to hypothetical proteins from C. elegans.
Further details of these data are shown in Table 3. BLAST analysis of the 37 clusters with a greater than two-fold difference in expression in the L1 stage, compared with the iL3 stage, shows that three have no significant alignment; seven have a significant alignment to hypothetical proteins from C. elegans and the remaining 27 have significant alignment to known C. elegans proteins (Table 4).
E-Predict computes a 'theoretical hybridization energy profile' for each complete viral genome, by using BLAST to align probes to the genome sequence, and then computing a predicted hybridization free energy for each probe having a significant alignment.
Of the 1,180,500 reads from the junco transcriptome used for this assembly, 1,031,427 (87%) had a significant alignment to the zebra finch genome identified by the software, with an average of 92.9% identity.
However, the model has a significant score preference for alignments that reach the end of a hairpin with no intervening unaligned sequence; without at least one well-conserved stem loop to anchor or seed the potential hit, the scores of these sequences are well down into the noise of scores from random sequences.
Determined by analogy to the orthologous human gene by ICCARE Linkage group Position of the quail fragment on the chicken genome sequence assembly, determined by BLASTN E-value of the quail-chicken alignment GCT1121 has a significant hit with chicken EST BI391579, that aligns with the chicken assembly at chrun:101609131 101609680 This BAC clone hybridizes to 1 chicken and 2 quail chromosomes.
This classifier computes a probability P SVM value that the input alignment has a significant evolutionary conserved secondary structure based on the thermodynamic stability of predicted structure and on sequence covariations consistent with a common structure.
We then calculated the mean L1 : iL3 fold difference in expression of these S. ratti ESTs that (i) had a significant BLAST alignment and (ii) did not have a significant BLAST alignment with the C. elegans genes, and compared these using a t-test (Table 8).
