The reads were then aligned to the mm10 genome assembly using NovoAlign requiring a minimum alignment length of 25 nucleotides (settings –s 1 –t 85 –l 25) (Novocraft, Malaysia).
The resulting alignments a ∈ A are used to generate the edges in G. Contigs v i and v j that overlap end-to-end with a minimum alignment length l A,min and maximum length l O,max of non-aligned overhang (Fig. 2), i.e. the part of the contig that will be clipped when merging the two, are then joined by a forward and a reverse edge, (v i, v j ) and (v j, v i ).
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.
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.
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.
Aligned the sequence reads to the Btau2.0 assembly (ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Btaurus/) after requiring unique mapping with high significance, i.e., a minimum alignment length of 500 bases with no gaps of more than 2 bp.
The EST alignments were filtered based on requirements for minimum alignment length and sequence identity in order to differentiate cases in which the amino acid sequences were supported by a strong alignment from the cases in which the alignment indicated a paralog rather than a direct validation of the sequence by genomic data.
