To exclude that these results were driven by the sequences gathered from Primates the calculations were repeated after excluding them from the dataset, with a similar outcome (Table 1).
These mtDNA sequences were compared with 98 additional mtDNA sequences gathered from various published collections.
This phylogenomic dataset was built by concatenating 106 alignments of DNA sequences gathered from 7 Saccharomyces species and Candida albicans as outgroup (see [ 77] for more details).
Because the genes sequenced on the 454 were targeted or known, a local database of related query sequences gathered from GenBank was constructed to perform a Blast (Altschul et al. 1990) search for each read from each file.
Although it is not possible to do an accurate PIC estimate just by using a collection of public sequences gathered from different heterogeneous projects, a rough index related to polymorphism might be calculated by counting the number of individuals in which each allele appears.
P. berghei EST (5,582) and GSS (5,482) sequences were gathered from the University of Florida P. berghei Genome Tag Sequences website in August 2004 [ 43].
As for the reference sets, ENSEMBL (version 68) is used for retrieval and classification of coding and non-coding RNAs, whereas protein sequences are gathered from the UniProtKB database (release 2012_11).
HIV sequence alignments were gathered from the LANL HIV Sequence Database, and processed according to [27], but here only subtypes A1, B, and C. We gathered 1436 proteins known to be phosphorylated from dbPTM [19], and found 132 of these were phosphorylated by ERK1/2.
Sequence conservation scores for each position were derived based on multiple sequence alignments of homologs gathered from the UniProt database (Apweiler et al., 2004) using PSI-BLAST (Altschul et al., 1997).
