Small modulation of ongoing cortical dynamics by sensory input during natural vision
The full-length cDNA data set was downloaded from http://cdna01.dna.affrc.go.jp/cDNA/ on 15 November 2003. A Pack-MULE is considered to have a cDNA match if, first, sequence similarity between the Pack-MULE and the cDNA is higher than 99.5% over the entire length of the cDNA and, second, the chromosomal position of the Pack-MULE is consistent with the genomic position of the particular cDNA provided by the rice fulllength cDNA consortium 19 . Peptide sequences representing 2,528 unique proteins
... were downloaded from ref. 20 (http://www.pnas.org) and used as queries to search against all Pack-MULE sequences recovered in both the genome-wide search and the search of chromosomes 1 and 10 with TBLASTN 20 . Peptide sequences that generated perfect hits with Pack-MULE sequences were then used to search the rice genomic database. A particular Pack-MULE sequence was considered to have a peptide match if it was the only perfect hit in the genome. K a /K s analysis The sequences of each Pack-MULE and its corresponding genomic homologue were aligned using the 'pileup' program from the University of Wisconsin GCG program suite (version 10.1) accessed through Research Computing Resources at the University of Georgia. The alignment was based on the ORF of the genomic homologue (see Supplementary Tables 6 and 10 for details). If the genomic homologue was not predicted as a coding sequence, the ORF of the MULE was used. K a and K s were calculated with MEGA using the Pamilo-Bianchi-Li method 24 . The significance of purifying selection (P value) was evaluated with the z-test in MEGA.