Biopython

The course content consists of two main parts. The first part deals with an introduction to python, the goal of which is to lay down the basics of algorithms and programming languages in general. The first part contains the following:

1. Install python, pycharm, and biopython.

2. Knowledge of basic syntax, which includes variables and line write methods in python.

3. Knowing the five variable types, which include number, string, list, tuple, and dictionary.

4. Knowing the operator types, including arithmetic, comparison, assignment, logical, membership, and identity.

5. Understanding decision-making strategies, including the use of “if .. else”, “if .. elif .. else” and “nested if.”.

6. Understanding loops, writing, and controlling while loop and for loop.

The second part is an introduction to biopython, which is a package based on python, so we will apply what was understood in the first part. The second part contains the following:

1. Dealing with the NCBI database through Entrez, requires an internet connection, and we will use einfo, espell, esearch, esummary, egquery, and efetch.

2. Working with files, writing, and converting files using seqio. dealing with the two most popular types of sequence files in terms of reading and writing in detail.

3. Working with sequences through python, they understand some functions such as slice, find, count, len, lower, upper, replace, split, join and strip.

4. Transcription of molecules as cell, transcription and reverse transcription of DNA and RNA respectively, DNA translation. manufacture of complement and reverse complement of DNA.

5. Simple basic analysis of sequences, including GC content, molecular weight, and six reading frames. search inside sequences using nt_search.

6. Pairwise alignment, understanding, and implementing both local and global alignment. work with results and understand matches and gaps.

7. Multiple sequence alignment, execute and read multiple sequence alignment and extract data for the phylogenetic tree.

8. Blast, sequence search in the NCBI database. build a local database and implement blast offline. dealing with results in detail.

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