sequence-extract

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• This project aim to extract each gene and intergenic regions from annotated -

•                    genomes to separated fasta files                      -
  

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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:

1. Sequence Fasta format
2. sequence genbank format

return:

1. separated genes in fasta format

2. 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:

1. Sequence Fasta format
2. sequence genbank format

return:

1. 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.