MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

Miniature inverted-repeat transposable elements (MITEs) are a special type of Class 2 non-autonomous transposable element (TE) that are abundant in the non-coding regions of the genes of many plant and animal species. The accurate identification of MITEs has been a challenge for existing programs because they lack coding sequences and, as such, evolve very rapidly. Because of their importance to gene and genome evolution, we developed MITE-Hunter, a program pipeline that can identify MITEs as well as other small Class 2 non-autonomous TEs from genomic DNA data sets. The output of MITE-Hunter is composed of consensus TE sequences grouped into families that can be used as a library file for homology-based TE detection programs such as RepeatMasker. MITE-Hunter was evaluated by searching the rice genomic database and comparing the output with known rice TEs. It discovered most of the previously reported rice MITEs (97.6%), and found sixteen new elements. MITE-Hunter was also compared with two other MITE discovery programs, FINDMITE and MUST. Unlike MITE-Hunter, neither of these programs can search large genomic data sets including whole genome sequences. More importantly, MITE-Hunter is significantly more accurate than either FINDMITE or MUST as the vast majority of their outputs are false-positives

Additional file 1 of lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals

Supplementary Tables and Figures. Supplementary Note 1: R code to compare lme4qtl and pedigreemm R packages. Supplementary Note 2: Multi-trait and multi-environment linear mixed models. Supplementary Note 3: R code applied to the GAIT2 data. (PDF 1341 kb

Measurement of the lepton charge asymmetry in inclusive WW production in pp collisions at s=7\sqrt{s} = 7 TeV

A measurement of the lepton charge asymmetry in inclusive pp to WX production at sqrt(s)= 7 TeV is presented based on data recorded by the CMS detector at the LHC and corresponding to an integrated luminosity of 36 inverse picobarns. This high precision measurement of the lepton charge asymmetry, performed in both the W to e nu and W to mu nu channels, provides new insights into parton distribution functions.A measurement of the lepton charge asymmetry in inclusive pp to WX production at sqrt(s)= 7 TeV is presented based on data recorded by the CMS detector at the LHC and corresponding to an integrated luminosity of 36 inverse picobarns. This high precision measurement of the lepton charge asymmetry, performed in both the W to e nu and W to mu nu channels, provides new insights into parton distribution functions.A measurement of the lepton charge asymmetry in inclusive pp to WX production at sqrt(s)= 7 TeV is presented based on data recorded by the CMS detector at the LHC and corresponding to an integrated luminosity of 36 inverse picobarns. This high precision measurement of the lepton charge asymmetry, performed in both the W to e nu and W to mu nu channels, provides new insights into parton distribution functions