The Python code and supporting material, including example data files, are
available as a single ZIP compressed archive. This must be uncompressed before
use and will extract into a folder (directory) called "PythonForBiology", inside
which the Python files, ending in ".py", and various sub-folders can be found.
This arrangement of files and folders will allow the Python code to run directly
from inside the uncompressed "PythonForBiology", i.e. the locations of any
modules or data files mentioned in the code (and book) are specified relative to
this location.
The "examples" sub-folder contains all of the data files that are used as
examples to support the Python code described in the book.
The "databases" sub-folder relates to Chapter 20 and contains SQL and Python
files sub-divided into sections to support both SQLite and MySQL database
implementations.
The "speedy" folder relates to Chapter 27 and contains code relevant to the
binding of fast functions written in the C or Cython languages, including any
files required for compilation.
Many of the book chapters have a corresponding Python file containing the
completed scripts and programs for that chapter. These files may be run directly
as Python to test the code they contain. Note that several of these files will
not work isolation, given that they import functionality from the others, which
are assumed to be in the same folder.
Chapters 1-4 and 10 do not have a corresponding Python file given that they only
discuss the code in terms of short or incomplete fragments.
2022-12-11 21:14:25
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参考文献：MUFOLD-SS: New deep inception-inside-inception networks for protein secondary structure prediction
目的：蛋白质二级结构预测。
上传原因：由于文献中的链接失效，因此将之前下载的开源源码上传。仅限学术研究使用。
2022-12-09 12:27:01
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生物工具
GTF.py
提供一个类，使您可以解析，重建仅由外显子组成的GTF或计算一些基本统计信息。
用法
从CLI
要仅从外显子重建完整的GTF（具有3个级别：基因，转录本和外显子），请使用以下命令，然后将重建的GTF打印到STDOUT
GTF.py format {gtf_path}
要计算您的GTF（仅包含外显子的GTF）中的基因，转录本和外显子的数量，请使用：
GTF.py stats {gtf_path}
从Python脚本
首先，导入GTF类。 此类提供了一种静态方法来解析您的文件：
您的GTF由3个级别的注释组成。 在这种情况下，请使用：
from GTF import GTF
for gene in GTF . parse ({ your GTF file }):
print ( gene )
您的GTF仅由外显子组成。 在这种情况下，请添加arg by
2022-12-03 14:48:00
3KB
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序列的多重比对是生物序列分析研究中的一个重要方法。文章首先介绍了HMM
的基本结构，然后着重讨论了HMM 在DNA 序列之间的多重比对中的应用。
2022-11-13 12:07:00
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有生物信息学的参考书；有文献数据挖掘的详细讲解；介绍文献编辑软件以及相关课堂练习；核酸，蛋白质序列分析以及数据分析以及相关上机操作的作业流程
2022-11-07 12:34:22
170.35MB
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