- This project aim to extract each gene and intergenic regions from annotated -
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genomes to separated fasta files -
The project consest of three main functions (gene_extract, intron_extract, and primer_pick_up) in addition to one assistance function (rc)
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(gene_extract) Function
This function determine the start and end of each gene according to GenBank annotation and extract each gene in an indvedual fasta file
input files:
- Sequence Fasta format
- sequence genbank format
return:
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separated genes in fasta format
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Number of genes at the input file
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(intron_extract) Function
This function determine the start and end of each gene according to GenBank annotation and extract the whole entergenic regions in a single fasta file
input files:
- Sequence Fasta format
- sequence genbank format
return:
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whole entergenic regions in a single fasta file
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(rc) Function
The function recieve DNA sequence and return sequence reverse complementary
input: DNA sequence
return: sequence reverse complementary
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(primer_pick_up) Function
The function Pick up sequences between forward and reverse primers from different files
Function name is (primer_pick_up)
inputs: 1.Forward_primer 2.Reverse_primer 3. numer_of_fasta_files: number of files the user need to test the primers on it
return: sequences between forward and reverse primers in fasta format file **********
Run Notes: The user should rename the tested sequence files to numbers started from 1, and put this file in the same folder with these python script.