Extract V3-V4 regions from 16s sequences

Question

[Florian Plaza Oñate]

Hi, I have a set of full-length 16s genes in a multi FASTA files. I am looking for a tool to extract all the v3-v4 variable regions. Thanks in advance.

[Florian Plaza Oñate]

Thanks. I will try it.

EDIT: It works very well. Thanks again.

[Picasa]

Just a question, how did you sequence full 16s genes ?

[Florian Plaza Oñate]

I have downloaded them from SILVA. I should change the question tags. However, I know that some labs get full length 16s with PacBio sequencers.

[Dattatray Mongad]

I had downloaded greengenes, SILVA and RDP full length 16S rRNA gene databases and used universal primers of V4 regions to scan against each sequence by fuzznuc (emboss toolkit). If required I can share my python script.

[samedsaka]

Could you please share your script?

Answer 1

[lakhujanivijay]

Check out V-Xtractor

Though, I never used.

Answer 2

[Dattatray Mongad]

You can find the script here. Just install emboss toolkit or make sure you have fuzznuc in your path. Let me know your experience, I will improve it if needed. This script uses given primer sets (reverse and forward) to extract the region which can be amplified. So you can use the primers accordingly. For example, here u can use forward primer fo V3 region and reverse primer for V4.

Usage:- python3.6 extract_n_multiplex.py [options] Options: -h, --help show this help message and exit -f FORWARD_PRIMER forward-primer -r REVERSE_PRIMER reverse-primer -n NITER (default 1) number of iterations to repeat random multiplexing of extracted sequences -d SEQDATA multifasta sequence file from which regions will be extracted.

[GenoMax]

Please add a bit more information to your post by editing it. What script are you referring to? What does it do? It would be useful to add that information in your post. is this script meant to be used to solve the original question posted in this thread?

[samedsaka]

I used your script. It works well. Thank you.

[nilaylale88]

Hello what are the primers you used, im getting an empty file? can you enlighten me please?

[Dattatray Mongad]

For my work, I have used modified primers for V4 (515f-806r) region of 16S rRNA gene as mentioned in Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

-f GTGYCAGCMGCCGCGGTAA -r GGACTACNVGGGTWTCTAAT

Answer 3

[liqing1123]

Dear all, I have got the same problem. I would like to extract all the v3-v4 region from silva.bacteria.fastq file. After consulting to the MISEQ SOP for mothur, I have used the command line as below. But I'm not sure about the start and end position for V3-V4 region. Can someone help to share their experience? Great appreciate for your help.

mothur "#pcr.seqs(fasta=silva.bacteria.fasta, start=6388, end=25319, keepdots=F,processors=8)"

Lola