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In one set of experiments, we evolved an expression pattern from a sequence that already drove a similar pattern, by choosing the initial sequence for each simulation randomly from one of the 5 CRMs whose expression is most correlated with the target expression pattern.
An initial sequence for 7096 [GenBank: AC204781] was assembled by the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) using the Phrap assembler [ 40] as part of the Atlas assembly system [ 41], with the traces from the randomly sheared subclone library [ 42].
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In view of our knowledge that pre-miRNAs may be located immediately downstream of SINEs, Pol-III-transcribed sequences are usually less than 500 bp in length and most SINE elements are less than 300 bp, we extended 200 bp downstream of SINEs as our initial sequences for predicting candidate miRNA genes.
Again, the encoder would transmit the code word for the initial sequence of levels and then an extra two bits for the last level.
This PCR method may be useful for obtaining templates for initial sequencing of novel orthoreoviruses from diverse vertebrate hosts.
A clone containing the nearly complete P. knowlesi gene encoding PkMSP-110/MSP-9 PkMSP-110/MSP-9 PkMSP-110/MSP-9and initial sequence information for the design of providedto obtain thybridizationnd probenomolgi orthologues using polymerand chainitialtion (PCR) amplification sequencees.
To obtain initial sequence information for the isolation of the wt1 gene, degenerate primers (Table 1 – wereF1a; WT1 R1a; WT1 F1b; WT1 R1b; WT1 F5) were designed based on coding sequences of this gene from D. rerio (NM_131046; NM_001039634), A. japonica (AB030741) and O. mykiss (AF334670; AF334670).
At this point, we re-evaluated the initial sequence pattern for PHI-BLAST because it was based solely on the sequence compilation of the Zic family genes.
However, they are not included in our initial sequence analysis for MAEL domains since they do not have MAEL specific residues (EHHCHC), and introducing these sequences may dilute conserved characteristics of MAEL domains.
Initial sequence alignment for these two systems was performed with the Clustal-W program [ 22], using the Blosum 30 substitution matrix, a gap-opening penalty of 10 and a gap-extension penalty of 0.1.
For initial sequencing of D. elegans HK and D. gunungcola SK, primer sequences were designed based on conserved regions among the genomes of the D. melanogaster species subgroup, D. ananassae, and D. pseudoobscura.
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