https://github.com/applicativesystem/go-alignment-estimate

a block basis estimate of the whole genome alignment estimates
https://github.com/applicativesystem/go-alignment-estimate

alignment-algorithm alignment-strategies bioinformatics genome-alignments genome-alignments-bioinfromatics genome-analysis phylogenmics-golang phylogenomics phylogenomics-bioinformatics

Last synced: 24 days ago
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a block basis estimate of the whole genome alignment estimates

• Host: GitHub
• URL: https://github.com/applicativesystem/go-alignment-estimate
• Owner: applicativesystem
• License: mit
• Created: 2024-09-18T19:15:12.000Z (4 months ago)
• Default Branch: main
• Last Pushed: 2024-09-29T07:50:01.000Z (3 months ago)
• Last Synced: 2024-11-10T20:18:08.485Z (about 2 months ago)
• Topics: alignment-algorithm, alignment-strategies, bioinformatics, genome-alignments, genome-alignments-bioinfromatics, genome-analysis, phylogenmics-golang, phylogenomics, phylogenomics-bioinformatics
• Language: Go
• Homepage:
• Size: 4.88 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# go-whole-genome-estimates

- a whole genome linear block estimation. 

- block is defined as a single line for the aligned genome. 

- no matter how many genome you aligned you can pass the alignment file.

- the first genome will be taken as a reference. 

- check the AlignmentGO package for defining your own block size. 

```

[gauravsablok@fedora]~/Desktop/codecreatede/whole-genome-alignment-estimate% \

go run main.go -alignment ./samplefile/samplealignment.fasta

The collinearity block for A as a base pattern and T as a mismatch is 1

The collinearity block for A as a base pattern G as a mismatch is  1

The collinearity block for A as a base pattern and C as a mismatch is 1

The collinearity block for T as a base pattern and G as a mismatch is 0

The collinearity block for T as a base pattern C as a mismatch is  0

The collinearity block for T as a base pattern and A as a mismatch is 0

The collinearity block for G as a base pattern and C as a mismatch is 1

The collinearity block for G as a base pattern A as a mismatch is  0

The collinearity block for G as a base pattern and T as a mismatch is 0

The collinearity block for C as a base pattern and A as a mismatch is 0

The collinearity block for C as a base pattern T as a mismatch is  0

The collinearity block for C as a base pattern and G as a mismatch is 0

```

Gaurav Sablok