https://github.com/jkanche/suffixtreealignment

local alignment using suffix tree
https://github.com/jkanche/suffixtreealignment

Last synced: 23 days ago
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local alignment using suffix tree

• Host: GitHub
• URL: https://github.com/jkanche/suffixtreealignment
• Owner: jkanche
• License: mit
• Created: 2019-04-29T16:40:42.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2019-05-15T02:36:18.000Z (over 5 years ago)
• Last Synced: 2024-10-30T19:12:30.577Z (2 months ago)
• Language: Go
• Homepage:
• Size: 864 KB
• Stars: 0
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
## Local alignment search using suffix tree

Note: Written in GOLANG, to download go for your operating system, visit [golang.org](https://golang.org/)

### Installation

The code depends on the [memviz](http://github.com/bradleyjkemp/memviz) package for visualizing data structures in memory as graphViz plots.

```

> go get github.com/bradleyjkemp/memviz

```

### Build

```

> cd suffixTree

> go build

```

This will generate a binary `./suffixTree`

### Usage

The binary generated from the previous step takes two arguments

- Text to build the suffix tree

- Query string to search

#### Building a Suffix Tree from text

```

> ./suffixTree mississippi

```

This prints a graphViz representation of the suffix tree. Install [GraphViz](https://graphviz.org/) or use [webgraphviz](http://www.webgraphviz.com/) to plot. If you have graphViz installed locally -

```

> ./suffixTree mississippi | dot -Tpng -o graph.png

```

![SUFFIX TREE](suffixTree/figure1.png "Suffix Tree for MISSISSIPPI$")

#### Search the suffix tree for a query string

The second argument to the suffix tree is the query string and will print all index positions where the string matches

```

> ./suffixTree mississippi issip

```

Note:

- can/might have bugs (yet to find one)

- has too many print statements (commented out)

After the output of the search of a query string Q in the suffix tree created from text T, use the Python code `extend_max_match.py` to extend the maximum exact match to obtain a local alignment. The script is written in [Python3](https://www.python.org/).

The script accepts all exact matches between Q and T, and builds a heuristic local alignment that is centered around the maximum exact match. Each line in the input file is formatted as: `[  ]`. All suffixes of the query string are matched and the longest exact matches are listed in the input.

Run the Python script as:

```

 > Python3 extend_max_match.py input_file.txt

 ```