Sequences were aligned using the alignment tool of the ARB package (http://www.arb-home.de/) and Bioedit software (http://www.mbio.ncsu.edu/BioEdit/bioedit).
As a control, the reads were first aligned using the alignment tool provided by Applied Biosystems (mapreads) against reference sequences representing the fully bisulfite converted Watson and Crick strands and the unconverted Watson strands of A.thaliana and phage lambda.
Different azo-reductase protein sequences from various microorganisms were aligned against those of B1 P. aeruginosa using the alignment tool of CLC Main Workbench 5 (CLC Bio, Aarhus, Denmark).
A multiple sequence alignment was constructed using the alignment tool in Geneious Pro version 6.1.6 (Drummond et al., 2011) before performing manual checks and minor adjustments.
We mapped the pig genome onto the human genome using the alignment tool (LAST) and found the syntenic region; the pig chromosomes are rearranged in human chromosome scale.
The sequence obtained was compared with sequences available in EMBOSS database via http://www.ebi.ac.uk/emboss/align/ using the alignment tool.
Mapping generating four total transcriptome profiles (Additional file 2) using the alignment tool TopHat version 2.02 [ 55] integrated with Bowtie version 0.12.7 [ 56].
Full-length 16S rRNA gene sequences (> 1300 bases) were added to an ARB alignment of about 28,000 small-subunit rRNA sequences by using the alignment tool ARB_EDIT of the ARB program package [ 37].
Students also reported strong increases in their confidence in using the alignment tools, Geneious and BLAST.
The Ensembl analysis and annotation pipeline uses the exonerate alignment tool [ 17] and tolerates only 1 base pair (bp) mismatch between the probe and the genome sequence assembly.
