zehramsa 1.0.3

Multiple Sequence Alignment via Dynamic Programming

Dil / Language: 🇹🇷 Türkçe · 🇬🇧 English

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zehramsa — Çoklu Dizi Hizalama Kütüphanesi

zehramsa, Needleman-Wunsch dinamik programlama algoritmasına dayalı progresif hizalama yaklaşımını kullanarak birden fazla DNA dizisini hizalayan, saf Python ile yazılmış bir kütüphanedir. Harici bağımlılık gerektirmez; pip ile kurulabilir.

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Teknolojiler

• Python 3.9+
• Needleman-Wunsch — global pairwise hizalama (dinamik programlama)
• Progresif MSA — NW tabanlı adım adım çoklu dizi birleştirme
• pyproject.toml — pip kurulum desteği

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Özellikler

• İkili dizi hizalama (Needleman-Wunsch DP)
• 2+ dizi için progresif NW tabanlı MSA
• Özelleştirilebilir puanlama (match / mismatch / gap)
• Sum-of-Pairs hizalama skoru hesaplama
• Hizalama kimlik yüzdesi hesaplama
• Tip ve girdi doğrulama ile açık hata mesajları

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Kurulum

pip install zehramsa

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Kullanım

Çoklu dizi hizalama

from zehramsa import align, SimpleScoring

result = align(["GATTACA", "GCATGCU", "GAGTACA"])
print(result)

result = align(["ACGT", "ACCT", "AGGT"], scoring=SimpleScoring(match=2.0, mismatch=-1.0, gap=-2.0))
print(result.score)

dp_align ile hizalama

from zehramsa import dp_align

result = dp_align(["GAT", "GCT", "GTT"])
print(result)

result = dp_align(["ACGT", "AGT", "ACT"], scoring=SimpleScoring(match=2.0, mismatch=-1.0, gap=-2.0))
print(result.score)

Needleman-Wunsch ikili hizalama

from zehramsa import needleman_wunsch

pw = needleman_wunsch("GATTACA", "GCATGCU")
print(pw)

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Algoritmalar

Fonksiyon	Yöntem	Karmaşıklık
align() / dp_align()	Progresif NW	O(k·n²)
needleman_wunsch()	Pairwise DP	O(n²)

align() ve dp_align() aynı algoritmayı çalıştırır; align() ek olarak verbose parametresi sunar.

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Süreç

Proje, dinamik programlama ile çoklu dizi hizalamasının sıfırdan uygulanmasına odaklanır. Önce Needleman-Wunsch algoritması ayrı bir modül olarak kuruldu; ardından 2+ dizi için progresif hizalama stratejisi entegre edildi. Her yeni dizi, referans diziye (ilk dizi) NW ile hizalanarak mevcut hizalamaya eklenir. Sum-of-Pairs skoru tüm kolon çiftleri üzerinden hesaplanır.

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zehramsa — Multiple Sequence Alignment Library

zehramsa is a pure Python library that aligns multiple DNA sequences using a progressive alignment approach based on the Needleman-Wunsch dynamic programming algorithm. No external dependencies required; installable via pip.

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Technologies

• Python 3.9+
• Needleman-Wunsch — global pairwise alignment (dynamic programming)
• Progressive MSA — NW-based step-by-step multi-sequence merging
• pyproject.toml — pip installation support

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Features

• Pairwise sequence alignment (Needleman-Wunsch DP)
• Progressive NW-based MSA for 2+ sequences
• Customizable scoring (match / mismatch / gap)
• Sum-of-Pairs alignment score calculation
• Alignment identity percentage calculation
• Type and input validation with clear error messages

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Installation

pip install zehramsa

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Usage

Multiple sequence alignment

from zehramsa import align, SimpleScoring

result = align(["GATTACA", "GCATGCU", "GAGTACA"])
print(result)

result = align(["ACGT", "ACCT", "AGGT"], scoring=SimpleScoring(match=2.0, mismatch=-1.0, gap=-2.0))
print(result.score)

Align with dp_align

from zehramsa import dp_align

result = dp_align(["GAT", "GCT", "GTT"])
print(result)

result = dp_align(["ACGT", "AGT", "ACT"], scoring=SimpleScoring(match=2.0, mismatch=-1.0, gap=-2.0))
print(result.score)

Pairwise alignment with Needleman-Wunsch

from zehramsa import needleman_wunsch

pw = needleman_wunsch("GATTACA", "GCATGCU")
print(pw)

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Algorithms

Function	Method	Complexity
align() / dp_align()	Progressive NW	O(k·n²)
needleman_wunsch()	Pairwise DP	O(n²)

align() and dp_align() run the same algorithm; align() additionally offers a verbose parameter.

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The Process

The project focuses on implementing multiple sequence alignment from scratch using dynamic programming. Needleman-Wunsch was built as a standalone module first; progressive alignment strategy was then integrated for 2+ sequences. Each new sequence is aligned to the reference sequence (first sequence) via NW and merged into the existing alignment. Sum-of-Pairs score is computed over all column pairs.