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We took into account sequencing errors in order to have a reliable reconstruction of the viral quasispecies on this region.
It is not uncommon to have only 50% of the reads mappable, though with more 'intelligent' mapping algorithms that take into account sequencing errors or polymorphisms, mappability has increased significantly.
The remaining sequences were analysed using ESTScan [ 14, 15], a web-based program that detects coding sequence by taking into account sequencing errors that frequently occur in single-pass sequences and can cause frame-shift mutations (174 clones).
Protein sequences can be predicted from the EST nucleotide sequence using programs such as ESTscan [[ 16] and [ 17]], which takes in to account sequencing errors and thus potential frame-shift mutations which are often present when there is only one EST sequence available for study.
The EdgeR package adjusted the analysis taking into account sequencing depths represented by library sizes.
We therefore divided datasets into sequencing bins by using thresholds of 1 million, 5 million, 12 million, and 24 million uniquely mapped reads (taking into account sequencing depths recommended in the past by the ENCODE consortium for TFs).
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I will focus on the design features of the accounts and account sequences: how the action accounted for is accomplished; how the account is formulated; what the placement of the account in the sequence is; and how the account is responded to.
Our tool, called RSpredict, takes into account sequence covariation and employs effective heuristics for accuracy improvement.
This process takes into account sequence similarity and the evidence code (EC) associated with GO annotations.
As a consequence, the distance takes indirectly into account sequence similarity and other genomic information.
[ 20] recently reported an algorithm to predict nucleosome positions that takes into account sequence composition and thermodynamic properties.
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