I have a GFF file containing positions of annotations (Transposons, mRNA, etc.), and the FASTA file of the reference genome (i.e. Vitis vinifera).
I would like to transfer the GFF into a FASTA file containing the sequences corresponding to the information included in the GFF.
Hi Giovanni if you don't want to install any software you can do it online with the Galaxy Platform. It is a really nice platform that you can use for a lot of other analysis.
For your particular problem, it's really easy!
1)Go to: https://main.g2.bx.psu.edu/
2)Click on Get Data on the left panel
3)select as a file format gff
4) add your gff file clicking choose file or paste it directly on the input
5) select your genome of reference and click execute
6)After it loads the file click on Fetch Sequences on the left panel and click Extract Genomic DNA using coordinate..
7) Click execute selecting your file and it will create a new fasta file for you with your sequences (see the right panel) that you can visualize on the browser or download
Good Luck!
Luca
http://about.me/lucapinello
Ciao Giovanni. The easiest way is to use bedtools with the option "getfasta". Here the link http://code.google.com/p/bedtools/
Best regards
You can try Readseq (http://www.ebi.ac.uk/Tools/sfc/readseq/) or EMBOSS-seqret (http://www.ebi.ac.uk/Tools/sfc/emboss_seqret/).
Hi Giovanni if you don't want to install any software you can do it online with the Galaxy Platform. It is a really nice platform that you can use for a lot of other analysis.
For your particular problem, it's really easy!
1)Go to: https://main.g2.bx.psu.edu/
2)Click on Get Data on the left panel
3)select as a file format gff
4) add your gff file clicking choose file or paste it directly on the input
5) select your genome of reference and click execute
6)After it loads the file click on Fetch Sequences on the left panel and click Extract Genomic DNA using coordinate..
7) Click execute selecting your file and it will create a new fasta file for you with your sequences (see the right panel) that you can visualize on the browser or download
Good Luck!
Luca
http://about.me/lucapinello
Thanks Luca. Do you know if Galaxy has upper limits for size of files (GFF) to be uploaded?
Dear Giovanni,
A PERL program with the help of regular expressions can solve such type of problems and in future you may not have to depend on any software. If you need I can help you in writing such a codes
Atul,
it must be great. I know that Perl or Python can do it, but I'm not able to program with them. Since I don't know if I will need this in the future, I will have a look at BEDTools and Galaxy before contacting you for a help in the script writing.
Many thanks in advance.
Dear Giovanni,
Any time you need me just let me know. Its my pleasure to contribute in research of Bioinformatics
Simple perl script using regular expressions can do ur work in 2 seconds ..
Just split the $_ field variable into strings... Add a ">" newline and ur work is done !
Goodluck..
Hi Giovanni,
You can use this software:
http://bioinformatica.genomatica.eu/GFF2GB.zip
Goodluck
Luca,
unfortunately, Galaxy does not include Vitis vinifera reference genome.
:(
Hi Giovanni, here the command line for bedtools.
bedtools getfasta -fi GENOME_FASTA -bed GFF_FILE -fo OUTPUT_FASTA -s
Giovanni,
Il programma che ho postato prima l'utilizzato col genoma di Vitis Vinifera.
you could try Bedtools's "fastaFromBed" module that needs an input Fasta and a Bed/GFF/VCF file and outputs the target Fasta file.
A program called gffread is included with the Cufflinks package and it can be used to verify or perform various operations on GFF files.
I was successfull with 'fastaFromBed'.
Now, the FASTA has 'chr1:1245-1299(-)' as header. I would like to include in the FASTA header the Name of the element which was present in the GFF file. Is it possible?
Augustus Gene prediction tool has a perl script in script directory, you can use that.
I am not sure what information is contained in GFF files (which you can download from NCBI ftp site). There aro also GBS files, which contain both sequences AND annotations. For vine you can get them at:
ftp://ftp.ncbi.nih.gov/genomes/Vitis_vinifera/Assembled_chromosomes/gbs
There is Python library named gbparsy using which you can extract lots of info
from gbs files:
http://code.google.com/p/gbparsy/
Best,
From a programmers point of view (and programming is very easy to do) all you need know is the formats of the two files, read one and write the other. This is not a hard problem to solve.
Hello, I am not a programmer and arrived here by googling a similar question to Giovanni's. Judging from many of the answers posted by people familiar with programming, it should be very easy to write a script (Perl, Python, Bioperl...). However, no one actually shared a script. Would anyone be so kind and do this so that people like me can learn by example?
You can use EMBOSS-seqret or Readseq.
For using via the internet, go to the EMBL-EBI Sequence Format Conversion tools:
- http://www.ebi.ac.uk/Tools/sfc/emboss_seqret/ or
- http://www.ebi.ac.uk/Tools/sfc/readseq/
For using local standalone versions, download the tools from:
- EMBOSS: ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
- Readseq: http://iubio.bio.indiana.edu/soft/molbio/readseq/java/
Hi Weizhong Li, thanks for your answer. I think it is a nice thing that there is such a variety of tools online. Just had a look at Readseq and I don’t see how I can tell it the coordinates of my features. I first thought that could be done using “Subrange” but no luck. Seqret seems to be a tool dedicated to format conversion; I don’t see how it should extract subsequences for me. Endless hours can go by just finding out how tools work and trying them and that is not efficient, and is also frustrating. That is why I asked the question here. Anyone a script to extract subsequences from a fasta file given a file with start and end coordinates?
You might be interested in bedtools: http://bedtools.readthedocs.org/en/latest/index.html
for getting fasta use "getfasta" fo bedtools..
Http://bedtools.readthedocs.org/en/latest/content/tools/getfasta.html
What if you blast your sequence in plain text with the same sequence using blast two sequence allignment and download your resulting match in a fasta format?
Hi, Giovanni, i met the same question as you,
https://www.researchgate.net/post/How_to_extract_kinds_of_datas_from_a_GFF_file_based_on_genome_fasta_who_can_help_me
can you help me to solve this prob?
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