Sentence examples for alignment version from inspiring English sources
Aligned sequences and a Greengenes reference alignment, version gg_13_5 (ftp://greengenes.microbio.me/ [last accessed April 19 , 2014]greengenes_release; [ McDonald et al. 2012]) were imported into the phylogenetic software package ARB (Ludwig et al. 2004), and the Melainabacteria sequence alignments were manually corrected using the ARB EDIT tool.
The nucleotide sequences were identified by BLAST search against GenBank databases and were compiled and aligned with the help of the Align Plus 4 for Windows 95 (Scientific and Educational Software, version 4.00) and ClustalX Multiple Sequence Alignment (version 1.81) programs.
Moreover, to find potential errors in the alignment, several models based on different alignment versions are usually built and analyzed in terms of parameters such as unfavorable burial of charged residues.
The PASS2 database [40] contains structure-based SCOP domain superfamily alignments (version 1.63) that have been derived using COMPARER [41] and STAMP [42].
Ensembl EPO 12-way alignments version 65 can be downloaded from the Ensembl (December 2011) at ftp://ftp.ensembl.org/pub/release-65/emf/ensembl-compara/epo_12_eutherian/ .org/pub/release-65/emf/ensembl-compara/epo_12_eutherian/ .org/pub/release-65/emf/ensembl-compara/epo_12_eutherian/
For a functional characterisation of the libraries, rpstBLASTn was used against the database of metazoan orthologies computed from eggNOG-alignments (version 2, [ 29]).
Sequences were assembled and aligned using Bioedit Sequence Alignment editor version 7.0.9.
Genomes were aligned using the MAUVE genome alignment program version 2.1.1 [ 32].
Pol sequences and env sequences >300 bp, were aligned in the BioEdit Sequence Alignment Editor Version 7.0.9.
Sequencing products were purified and underwent electrophoresis with the 3100 Genetic Analyzer (Applied Biosystems) and aligned by using the multisequence alignment CLUSTALX version 1.8 (13 ).
Amino acid sequences were obtained using the BioEdit Sequence Alignment Editor version 7.0.5.2 [ 37] and aligned using the Clustal W program.
