Sentence examples for frame identified using from inspiring English sources

HMM (hidden markov model) protein families from the PFAM [ 65] and TIGR [ 66] databases were assigned to the amino acid translation of the most likely reading frame (identified using an open reading frame prediction tool [ 67]) of each transcript using HMMscan [ 68] under default settings.

The longest open reading frame was identified using EMBOSS: getorf (http://emboss.open-bio.org/wiki/Appdocs) to identify all open reading frames and a custom Perl script to retain only the longest.

The LOC_Os01 g68850 open-reading frame was identified using FGENESH and contained a high amount of repetitive elements.

The azimuthal orientation of the crystals with respect to the AFM image frame was identified using an optical microscope above the AFM cell.

Sequence assembly was done with Sequencher (Gene Codes, Ann Arbor, MI, USA) and open reading frames were identified using the ORF finder program at NCBI (http://www.ncbi.nlm.nih.gov/projects/gorf/). Sequence from a portion of a putative 5' LTR was identified in addition to sequence containing regions similar to pol genes from retrotransposons.

The open reading frames were identified using the WU-BLAST2 program.

Potential ORFs (open reading frames) were identified using the ORF-predictor server (http://proteomics.ysu.edu/tools/OrfPredictor.html) [ 33].

The sequence data were assembled using Roche's Newbler assembler, version 1.1.03.24, and open reading frames were identified using GLIMMER3 (Delcher et al. 1999) and the 'getorf' module of the EMBOSS package (Rice, Longden, and Bleasby 2000).

Open reading frames were identified using an in-house-developed program based on 'GetORF' from EMBOSS [ 142], and the annotation was performed through BLAST searches against the Swiss-Prot and GenBank databases with an E-value cutoff of 1E-3.

To obtain single best orthologs to human RefSeq proteins, as in the UCSC human 100 species multiple alignment track [ 105], Trinity FASTA files of the bowhead whale kidney (n=4) and liver (n=3) were concatenated and putative open reading frames (ORFs) identified using the Perl script TransDecoder bundled with Trinity [ 13].

For each predicted gene region, the longest open reading frame (ORF) was identified using ORF Finder with default values [ 38].