CleaveLand

[…] then used to predict cleavage sites. the pure reads with 20 and 21 nucleotides were used to identify potentially cleaved targets by paresnip (http://srna-workbench.cmp.uea.ac.uk/tools/paresnip/) and cleaveland 3.0 (http://sites.psu.edu/axtell). the targets predicted were classified into five categories (0, 1, 2, 3 and 4) according to the previous study []. based on the expression characteristics […]

[…] instructions. the extracted sequencing reads were stored in file samplea_rawdata.txt and were then used in e standard data analysis, which is described in . a publicly available software package, cleaveland3.0, was used to analyze the sequencing data generated. the key functions performed by this software and the relevant analysis results are described by ., gene ontology (go) annotations […]

[…] genes in tomato. tomato transcripts (cdna library, version 2.4/2.3) were used as data sets. the degradome sequencing library of tomato inoculated with p. infestans was used to verify the targets. cleaveland software was used to find the cleavage site of the mir482b targets,. t-plot figures were produced based on r language., the abundance of mir482b in tomato was examined by qrt-pcr. […]

[…] ends protocol, and sequenced using illumina hiseqtm 2500 sequencing platform (illumina inc.; san diego, ca, usa) at the beijing genomics institute (bgi) (shenzhen, china). a public software package, cleaveland3.0 was used for analyzing sequencing data. all the putative target genes were used as queries to align against lilium rna sequences. the true mirna cleavage sites from background noise […]

[…] rotary shaker at 300 rpm. in addition, a red fluorescent protein (rfp)-expressing a. fumigatus af293 strain used in this study was obtained from prof. eric pearlman (case western reserve university, cleaveland, oh, usa)., bone marrow-derived dendritic cells were generated by culturing mouse bone marrow extracted by flushing the femurs and tibias. the collected bone marrow was treated […]