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R2012a Documentation → Bioinformatics Toolbox
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Contents

Index

• Getting Started

• User's Guide

• Functions

• Constructor

• Data Formats and Databases

• Data Visualization

• Trace Tools

• Sequence Conversion

• Sequence Statistics

• Sequence Visualization

• Pairwise Sequence Alignment

• Multiple Sequence Alignment

• Scoring Matrices

• Phylogenetic Tree Tools

• Phylogenetic Tree Methods

• Graph Theory

• Graph Visualization Methods

• Gene Ontology

• Gene Ontology Methods

• Protein Analysis

• Profile Hidden Markov Models

• Microarray File Formats

• Microarray Utilities

• Microarray Data Analysis and Visualization

• Microarray Normalization and Filtering

• BioIndexedFile Methods

• BioRead Methods

• BioMap Methods

• GFFAnnotation Methods

• GTFAnnotation Methods

• HeatMap Methods

• Clustergram Methods

• ExpressionSet Methods

• ExptData Methods

• DataMatrix Methods

• MetaData Methods

• MIAME Methods

• Statistical Learning

• Mass Spectrometry

• Bioanalytics

Examples

• Release Notes

align2cigar - Convert aligned sequences to corresponding Compact Idiosyncratic Gapped Alignment Report (CIGAR) format strings

Syntax

[Cigars,Starts] = align2cigar(Alignment,Ref)

Description

[Cigars,Starts] = align2cigar(Alignment,Ref) converts aligned sequences represented in Alignment, a cell array of aligned strings or a character array, into Cigars, a cell array of corresponding CIGAR strings, using the reference sequence specified by Ref, a string. It also returns Starts, a vector of integers indicating the start position of each aligned sequence with respect to the ungapped reference sequence.

Input Arguments

`Alignment`	Cell array of aligned sequence strings or a character array representing aligned sequences. Soft clippings are assumed to be represented by lowercase letters in the aligned sequences. Skipped positions are assumed to be represented by . in the aligned sequences.
`Ref`	String specifying an aligned reference sequence. The length of `Ref` must equal the number of columns in `Alignment`.

Output Arguments

`Cigars`	Cell array of CIGAR strings corresponding to each aligned sequence in `Alignment`.
`Starts`	Vector of integers indicating the start position of each aligned sequence with respect to the ungapped reference sequence.

Examples

Create a cell array of aligned strings, create a string specifying a reference sequence, and then convert the alignment to CIGAR strings:

aln = ['ACG-ATGC'; 'ACGT-TGC'; '  GTAT-C']

aln =

ACG-ATGC
ACGT-TGC
  GTAT-C

ref =  'ACGTATGC';
[cigar, start] = align2cigar(aln, ref)

cigar = 

    '3M1D4M'    '4M1D3M'    '4M1D1M'


start =

     1     1     3

References

[1] Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Goncalo, A., and Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 16, 2078–2079.