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A tool to extract variable regions from 16S gene sequences

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Extract regions from 16s gene sequences

This tool extract variable regions from the 16S rRNA gene.

Summary

Installation

git clone https://github.com/AlessioMilanese/extract_regions_16s.git
cd extract_regions_16s

Note: in the following examples we assume that the python script extract_regions is in the system path.

Pre-requisites:

Simple example

The expected input is a fasta file with one (or more) 16S sequences, example:

cat my_16S_seq.fasta
>seq1
CAGTATTAGCGGGGATCATCGATCGATTACGATCGAGCTAGC....
>seq2
CAGTATGATCGCGGATCATCGATCGATTACGATCCAGCTAGG....

Running:

extract_regions -i my_16S_seq.fasta

results is:

>seq1__V1
ACACAGCAUGCAUAACACGAGCUAUCGACGACUACGACGGCA
>seq1__V2
CAUCAGUACCGAUCAUCGGAAUCAGCGAGGCAGGCGAAGGCGAGAGAGCAUAC
...
>seq1__V8
ACUACGUGCACGAGUACGUAUACGGACAUCGAUUUACGAGCAGCGA
>seq1__V9
ACAGAUCGGAUUCGAUCGGCAUCGGACCCAUCAGGAGGAUCGUCAAUCAUG

Mode 1: extract variable regions

If you don't specify any primer (with -f and -r), then all the variable regions will be extracted. We extract the variable regions defined in Yarza et al. Nat. Rev. Microbiol. (2014):

Variable region Start End
V1 69 99
V2 137 242
V3 433 497
V4 576 682
V5 822 879
V6 986 1043
V7 1117 1173
V8 1243 1294
V9 1435 1465

These positions refers to the 16S rRNA gene of Escherichia coli str. K-12. The output is a fasta file with 9 times more sequences (one for each variable region) than the input fasta file.

The regions are indicated with __V[1-9] at the end of the fasta header (see also Simple example).

Mode 2: extract from primers

You can specify which primers to use with -f and -r.

For Primer Start End Relative position Rev Primer Start End Relative position
8F 8 27 before V1 338R 338 355 after V2
27F 8 27 before V1 519R 519 536 after V3
68F 49 68 before V1 785R 785 805 after V4
341F 341 357 before V3 806R 787 806 after V4
515F 515 533 before V4 907R 907 926 after V5
967F 967 985 before V6 926R 907 926 after V5
1237F 1220 1237 before V8 1100R 1100 1115 after V6
1391R 1391 1407 after V8
1492R 1492 1510 after V9

If you run on the fasta file defined before (my_16S_seq.fasta with two sequences) using extract_regions -i my_16S_seq.fasta -f 8F -r 338R you will obtain:

>seq1
AGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGUACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGA
>seq2
CGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGUACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGA

Where the header is the same as the original fasta file.

Mode 3: extract based on positions

You can specify the exact position that you want to extract with -f and -r.

For example, if you want to extract all the sequences of primer 8F, you can run extract_regions -i my_16S_seq.fasta -f 8 -r 27, which will result in:

>seq1
AGAGUUUGAUCAUGGCUCAG
>seq2
CGAGUUUGAUCAUGGCUUCAG

Note that the positions are based on the E.coli K12 16S gene.

Notes and advance usage

Details of implementation

Options list

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A tool to extract variable regions from 16S gene sequences

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