Submission

Paste in one or more GenBank file(s) Upload file containing one or more GenBank entries
View example GenBank file
Notice: Multiple GenBank format files can be concatenated. A comprehensive source for GenBank files is the NCBI web-site: `http://www.ncbi.nlm.nih.gov/`. Mar 13th, 2017:Light version (automatic look-up of GenBank IDs disabled).

Instructions: Basic usage - Paste in or upload a set of GenBank format files and hit submit. The FeatureExtract server will then by default extract all protein coding genes with full intron/exon annotation. Please read the DTU Health Tech access policies for information about limitations on the daily number of submissions. For processing large datasets (e.g the Human Genome builds from NCBI) it is recommended to download the command-line version of FeatureExtract from the "Software download" page, and do the processing locally.

Basic options
Select type of features to extract Alternatively, enter the desired feature type(s) below: Example: `CDS,rRNA,tRNA` Include intergenic regions. [details]	Naming preferences 1) Gene name 2) Systematic name 3) EntryId + distance If the desired type of naming is not available, fall back to the level below: 1 -> 2 -> 3. [details]	Flanking regions bp : Upstream (5') bp : Downstream (3') Optional: Define flanking regions [details]

Advanced options
Frameshifts (bp): Frameshift cutoff "Introns" shorter than this length are considered annotated frameshifts [details]	Custom defined annotation Example: `snRNA=(N),promoter={P},unknown=QQQ` [details]	Splicing (new in 1.2) Splice all intron containing seqeunces Full length sequences are kept in the comments field Only output intron containing sequnces Can be used in combination with the "splice all..." option [details]
Feature types to annotate in flanking regions Alternatively, enter the desired feature type(s) below: Example: `MOST,polyA` [details]	Flanking region annotation scheme Full annotation Uppercase = same strand, Lowercase = opposite strand. Presence/absence annotation + = same strand, - = opposite strand, # = overlapping [details]	Trouble shooting Produce verbose information Verbose: Output additional information about the contents of the GenBank files and the general progress of the extraction. [details]

Restrictions: A maximum of 100mb of GenBank files will be processed in each run.

Confidentiality:
The sequences are kept confidential and will be deleted after processing.

For publication of results, please cite:

The commandline version of FeatureExtract is open source software (GPL license) and can be downloaded on the "Software download" page.

If you require FeatureExtract on a commerical license, please contact software@cbs.dtu.dk.

Basic options