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If there is more than one such sequence, is set to be the smallest sequence index.
The limited functional diversity of the smallest sequence neighborhoods we examine likely results from this sparsity.
If sequences were more than 90% identical and overlapped more than 80% (of the smallest sequence), they were clustered together.
If sequences were more than 90% identical and overlapped by more than 80% (of the smallest sequence), they were grouped together.
To reduce sequencing efforts from samples, the smallest sequence numbers were selected to measure the alpha diversity, such as observed OTUs, the Shannon index, and rarefaction curves.
The protein similarity network was calculated using BLASTp with a minimal e-value threshold of 1E−40, 20% minimal similarity covering at least 20% of the smallest sequence.
Similar(50)
Increasing the adopted average tract length of 100 bp detects less putative recombination events by missing many of the smaller sequence inserts, while further decreasing this value does not change the results.
The smaller sequence database also narrows the phylogenetic context within which new data sets can be analyzed, and makes it more difficult to assemble the crucial copy-number information that would prevent misinterpretation of unsuspected variation among paralogs.
We found that only half of the small sequence differences actually present were reported as SNPs.
The only other universally conserved motif in this segment is the small sequence at the C-terminal extremity.
Clearly, a physical map is demanded for scaffolding the small sequence contigs into scaffolds, and eventually into chromosome-scale sequence assemblies.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com