To accommodate possible biases of this read mapping approach, additional DNA and RNA-seq read mappings were performed with CLC Genomics Workbench v 6.5 (mapping parameters: minimum 90% of read aligned and minimum alignment identity 95%), and resulting polymorphisms compared.
Orthologs were defined as proteins that were reciprocal best matches when all proteins from both genomes were aligned, with a minimum alignment of 60% of both proteins.
¥ Lowest common ancestor (LCA) using 1e-5 cutoff, 60% minimum identity, and a minimum alignment lenght cutoff of 15.
The parameters for inclusion were a maximum e-value cutoff of 1e-05, a minimum identity of 60%, and a minimum alignment length of 15.
Sequences enclosing tandem repeat sequences were recognized using Tandem Repeats Finder version 4.07b (Benson [1999]) by general setting on 2, 3, and 5 of match, mismatch, and indel for alignment parameters and 20 for minimum alignment score to report repeat.
To study specific metabolic pathways, the BA and RJ metagenomes were compared using 1e-05 as the maximum e-value cutoff, with a minimum identity of 60% and a minimum alignment length of 15.
At the end of the video, the path identifier held by the token with the minimum alignment cost allows the best event sequence to be traced back and the corresponding boundaries recovered.
This search identified 708 hits (Eminimum alignment length >50 bp).
Minimum alignment length coverage (-L parameter) varied between 0.1 and 0.9 with step size 0.1.
An e-value cut-off of 1×10−10 and a minimum alignment length of 50 basepairs were applied.
Ratios well below unity can be considered hits inside gene families or low scoring false positives, only as the minimum alignment length increases can the validity of the assignment be reasonably certain.
