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show-aligns

By Salzberg S., Delcher A., Last update 1494698999
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show-aligns description

Show-aligns parses the delta encoded alignment output of NUCmer and PROmer, and displays the pair-wise alignments from the two sequences specified on the command line. It is handy for identifying the exact location of errors and looking for SNPs between two sequences. Output is slightly different depending on the type of alignment, i.e. nucleotide or amino acid. Each alignment is preceded with a header containing the BEGIN keyword, the frame-direction information and the start and end in the reference and query respectively. Each individual line of the alignment is prefixed with the position of the first base on that line, these positions reference the forward strand of the DNA sequence regardless of alignment type. Errors in nucleotide alignments are marked with a *^* character below the two mismatching sequence bases. Errors in protein alignments are noted with a whitespace in between the two mismatching acids, while similarities (positive alignment scores) are marked with a *+* and identities are noted with a copy of the matching acid. Each alignment is followed by a footer containing the END keyword, the frame-direction information and the start and end in the reference and query respectively. Perhaps the best way to explain this format is by example, so snippets of the two types of alignments are given below.


Parent program: MUMmer

MUMmer or 'Maximal Unique Matches' is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure and is one of the fastest and most efficient systems available for this task, enabling it to be applied to very long sequences. It has been widely used for comparing different genomes to one another. In recent years it has become a popular algorithm for comparing genome assemblies to one another, which allows scientists to determine how a genome has changed after adding more DNA sequence or after running a different genome assembly program.