https://github.com/kentwait/conspos
Computes the consensus alignment between global, local and sub-global multiple sequence alignments
https://github.com/kentwait/conspos
Last synced: 5 months ago
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Computes the consensus alignment between global, local and sub-global multiple sequence alignments
- Host: GitHub
- URL: https://github.com/kentwait/conspos
- Owner: kentwait
- License: apache-2.0
- Created: 2017-08-09T05:41:19.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2019-04-25T07:37:25.000Z (about 7 years ago)
- Last Synced: 2024-06-21T02:17:48.158Z (about 2 years ago)
- Language: Go
- Homepage:
- Size: 815 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# ConsPos
[](https://travis-ci.org/kentwait/conspos)
[](https://coveralls.io/github/kentwait/conspos?branch=master)
Computes the consensus alignment by comparing alignment patterns
of global, local and sub-global multiple sequence alignments generated
by the alignment program [MAFFT][1].
## Quickstart
### Align a set of nucleotide or protein sequences in a single FASTA file
conspos input.fa > output.aln
### Align multiple FASTA files located in a single folder
conspos -batch path/to/folder -outdir path/to/save/alignments
## Background
ConsPos uses the multiple alignment program [MAFFT][1] to create three
multiple sequence alignments from one set of unaligned sequences using
three different alignment strategies - global alignment based on the
Needleman–Wunsch algorithm, local alignment based on the
Smith–Waterman algorithm, and local with affine-gap penalty scoring.
Even if these alignments were based on the same set of sequences, the
result could be vastly different. Thus, it is important to identify sites
that align robustly regardless of the alignment model used. We call
robustly aligning sites "consistent sites" and sites which exhibit mixed
patterns "inconsistent sites".
## Method
ConsPos identifies consistent sites by comparing the all alignment patterns
generated by the three strategies. It marks sites as "consistent" if the
particular alignment is rendered in all the given strategies. If the
particular alignment is not obeserved in all the alignment strategies
used, that site is marked "inconsistent". ConsPos creates a marker sequence
at the head of the generated FASTA-formatted alignment to mark the status of
each site.
## Example - consistent sites
Here is an unaligned set of 5 sequences. Our aim is to find out if different
alignment strategies will affect the resulting alignment.
#### Unaligned
>mel01
gtaagtgtacacattatttccgatgtgggccttttgacgacaaaagaaatttatag
>mel02
gtaagtgtacacattatttccgatgtgggccttttgacgacaaaagaaatttatag
>sim
gtaagtgtacacattatttcggatgtgggtcttttgacgacaaagacatttatag
>yak
gtatgtgtacacgttatttctaatgtgaaacttttaacgacgaagacatttctag
>ere
gtaagtgtacacgttatttctaatgtgaaacttttgacgacaaaagacatttatag
The following are results of iterative global (G-INSI), local (L-INSI), and
affine-gap penalty (E-INSI) alignments.
#### Global alignment
>mel01
gtaagtgtacacattatttccgatgtgggccttttgacgacaaaagaaatttatag
>mel02
gtaagtgtacacattatttccgatgtgggccttttgacgacaaaagaaatttatag
>sim
gtaagtgtacacattatttcggatgtgggtcttttgacgac-aaagacatttatag
>yak
gtatgtgtacacgttatttctaatgtgaaacttttaacgac-gaagacatttctag
>ere
gtaagtgtacacgttatttctaatgtgaaacttttgacgacaaaagacatttatag
#### Local alignment
>mel01
gtaagtgtacacattatttccgatgtgggccttttgacgacaaaagaaatttatag
>mel02
gtaagtgtacacattatttccgatgtgggccttttgacgacaaaagaaatttatag
>sim
gtaagtgtacacattatttcggatgtgggtcttttgacgac-aaagacatttatag
>yak
gtatgtgtacacgttatttctaatgtgaaacttttaacgac-gaagacatttctag
>ere
gtaagtgtacacgttatttctaatgtgaaacttttgacgacaaaagacatttatag
#### Affine-gap alignment
>mel01
gtaagtgtacacattatttccgatgtgggccttttgacgacaaaagaaatttatag
>mel02
gtaagtgtacacattatttccgatgtgggccttttgacgacaaaagaaatttatag
>sim
gtaagtgtacacattatttcggatgtgggtcttttgacgac-aaagacatttatag
>yak
gtatgtgtacacgttatttctaatgtgaaacttttaacgac-gaagacatttctag
>ere
gtaagtgtacacgttatttctaatgtgaaacttttgacgacaaaagacatttatag
Based on these three alignments, we can conclude that all sites are consistent
across different alignment strategies because the three methods produced the
exact same alignment.
#### ConsPos alignment
This is the summarized alignment produced by ConsPos. The first sequence
represents the status of each site after comparing between the different
strategies. Here, consistent sites are marked by "C" and inconsistent sites
are marked by "N". Because all sites are consistent, all characters in the
marker sequence are "C".
>marker
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
>mel01
GTAAGTGTACACATTATTTCCGATGTGGGCCTTTTGACGACAAAAGAAATTTATAG
>mel02
GTAAGTGTACACATTATTTCCGATGTGGGCCTTTTGACGACAAAAGAAATTTATAG
>sim
GTAAGTGTACACATTATTTCGGATGTGGGTCTTTTGACGAC-AAAGACATTTATAG
>yak
GTATGTGTACACGTTATTTCTAATGTGAAACTTTTAACGAC-GAAGACATTTCTAG
>ere
GTAAGTGTACACGTTATTTCTAATGTGAAACTTTTGACGACAAAAGACATTTATAG
## Example - inconsistent sites
What happens if the alignment strategies produce different results?
The following example shows how alignments can change based on the
method used.
#### Unaligned
>mel01
gtaagatagtggcagattaattattagagtatctgcaacatgaatattatcttaacag
>mel02
gtaagatagtggcagattaattattagagtatctgcaacatgaatattatcttaacag
>sim
gtaagataatggcagattaaacattagattatctgcaacaagaatattatctcgacag
>yak
gtaagtctgtggcaggttaataattattataatatttgcaataacaatattttctgaacag
>ere
gtaagccagtggcaggttaataatcagtatatttgcaacaacaataattcctcaatag
#### Global alignment
>mel01
gtaagatagtggcagat---taattattagagtatctgcaacatgaatattatcttaacag
>mel02
gtaagatagtggcagat---taattattagagtatctgcaacatgaatattatcttaacag
>sim
gtaagataatggcagat---taaacattagattatctgcaacaagaatattatctcgacag
>yak
gtaagtctgtggcaggttaataattattataatatttgcaataacaatattttctgaacag
>ere
gtaagccagtggcaggt---taataatcagtatatttgcaacaacaataattcctcaatag
#### Local alignment
>mel01
gtaagatagtggcagat---taattattagagtatctgcaacatgaatattatcttaacag
>mel02
gtaagatagtggcagat---taattattagagtatctgcaacatgaatattatcttaacag
>sim
gtaagataatggcagat---taaacattagattatctgcaacaagaatattatctcgacag
>yak
gtaagtctgtggcaggttaataattattataatatttgcaataacaatattttctgaacag
>ere
gtaagccagtggcaggt---taataatcagtatatttgcaacaacaataattcctcaatag
#### Affine-gap alignment
>mel01
gtaagatagtggcagattaattattaga---gtatctgcaacatgaatattatcttaacag
>mel02
gtaagatagtggcagattaattattaga---gtatctgcaacatgaatattatcttaacag
>sim
gtaagataatggcagattaaacattaga---ttatctgcaacaagaatattatctcgacag
>yak
gtaagtctgtggcaggttaataattattataatatttgcaataacaatattttctgaacag
>ere
gtaagccagtggcaggttaataatcagt---atatttgcaacaacaataattcctcaatag
In this case, the affine-gap method produced a different alignment compared
to the global and local alignments. Thus we observe that gap moves around the
middle portion of the alignment while the rest of the alignment remains the
same.
#### ConsPos alignment
>marker
CCCCCCCCCCCCCCCCCNNNNNNNNNNNNNNCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
>mel01
gtaagatagtggcagattaattattaga---gtatctgcaacatgaatattatcttaacag
>mel02
gtaagatagtggcagattaattattaga---gtatctgcaacatgaatattatcttaacag
>sim
gtaagataatggcagattaaacattaga---ttatctgcaacaagaatattatctcgacag
>yak
gtaagtctgtggcaggttaataattattataatatttgcaataacaatattttctgaacag
>ere
gtaagccagtggcaggttaataatcagt---atatttgcaacaacaataattcctcaatag
ConsPos detects these inconsistencies between alignments and marks these
inconsistent sites with the character "N" in the marker sequence.
## Installation
### Requirements
- MAFFT must be installed in your system. ConsPos does not include MAFFT.
- MAFFT must be included in the $PATH variable and executable from the shell.
This means that the program can be started in any directory by simplying
typing `mafft` from the command line.
ConsPos is available as a compiled binary for Mac and Linux operating
systems.
- [Mac][2] - Compiled and tested on MacOS 10.11.6
- [Linux][3] - compiled and tested on Ubuntu Linux
For other systems, its possible to compile the program from source
using `go build`. Note that you must have [Go][4] installed in your system
to compile this program.
## Links
- [MAFFT download page][1]
- [ConsPos for MacOS][2]
- [ConsPos for Linux (compiled on Ubuntu 16.04 x86-64)][3]
[1]: http://mafft.cbrc.jp/alignment/software/
[2]: https://github.com/kentwait/conspos/releases/download/v1.0.1/conspos
[3]: https://github.com/kentwait/conspos/releases/download/v1.0.1/conspos_linux_amd64