生物序列比对动态规划算法的统一形式化构造与Isabelle验证.pdfVIP

计算机研究与发展

Journal

of

Computer

Research

and

Development62（1）：119−131，2025

生物序列比对动态规划算法的统一形式化构造与Isabelle验证

石海鹤蓝孙文刘日明石海鹏王岚钟林辉111211

1

（江西师范大学计算机信息工程学院南昌330022）

2

（江西师范大学软件学院南昌330022）

（haiheshi@）

UnifiedFormalConstructionandIsabelleVerificationoftheDynamicProgramming

AlgorithmsforBiologicalSequenceAlignment

1

1

1

2

1

1

Shi

Haihe,

Lan

Sunwen,

Liu

Riming,

Shi

Haipeng,

Wang

Lan,

and

Zhong

Linhui

1

（SchoolofComputerInformationEngineering,JiangxiNormalUniversity,Nanchang330022）

2

（SchoolofSoftware,JiangxiNormalUniversity,Nanchang330022）

AbstractSequence

alignment

is

a

classical

problem

in

biological

sequence

analysis,

aiming

to

find

out

the

similarity

between

sequences,

which

is

of

great

significance

for

discovering

functional,

structural

and

evolutionary

information

in

biological

sequences.

The

problem

can

be

divided

into

two

categories:

pairwise

sequence

alignment

and

multiple

sequence

alignment.

The

existing

work

is

focused

on

specific

algorithms,

and

no

general

solution

is

designed.

In

addition,

there

are

few

researches

on

the

trustworthy

of

algorithms.

By

deeply

analyzing

the

properties

of

sequence

alignment

problem

and

describing

the

essential

characteristics

of

problem

solving,

a

unified

construction

framework

of

sequence

alignment

dynamic

programming

algorithm

seqAlign

is

designed

based

on

the

problem

formal

specification

and

formal

method

PAR.

The

process

of

constructing

a

multiple

sequence

alignment

algorithm

with

three

sequences

by

using

the

framework

is

f