Clustering was carried out using a strategy based on BLAST Basic Local Alignment Search Tooll) to identify candidate sequences (cut off e-value set to e-10) to be included in a cluster and Cap3 [ 62] to perform the assembly and produce the consensus sequences.
42 The novel targets were subjected to BLASTP against these proteomes at e-value cut off 10−5, sequence identity >35%, bit score >100 with BioEdit software.
A total of 137 operational taxonomic units (OTUs) were detected (using 97% similarity cut off during sequence clustering) and well-known ECM genera such as Cenococcum, Cortinarius, Hebeloma, Inocybe and Tomentella occurred frequently.
The BioEdit Sequence Alignment Editor (version 7.1.3) was used for Protein Basic Local Alignment Search Tool BLASTPP) search to screen for and eliminate the probable essential proteins of the organism setting e-value cut off 10−4, sequence identity >35%, bit score >100 and others as default.
Only 9 GIs are now compositionally more similar to the host genome when compared to the cut-off sequence CI-5.
The mitochondrial proteins were aligned with the protein sequences involved in, experimentally known, protein interactions using BLAST (cut-off sequence identity of 80%).
With this more lenient threshold, a total of 16 GIs are now compositionally more similar to the host genome than the cut-off sequence CI-25 is to the genome.
For this goal, we developed a suite of scripts that allows users to customize these analyses by modifying the minimal GI length, or the similarity cut-off sequence (i.e., the genomic Core Island of each genome with a certain genomic compositional dissimilarity).
A total of 62 PDB templates with different E-value cut offs for amino acid sequence similarity with BRP44 were obtained from PDB advanced search interface.
The operation unit (OTU) with 97% similarity and clustering cut off the Chimerical sequences was used to identify and exclude with UPARSE (7.1Version http://drive5.com/uparse/).
A total of 41,350 alfalfa unique sequences (76%) had a blastn hit to 24,358 MtGI sequences (cut off E value 1e-).
