DNannotator is a DNA sequence annotation tool kit.
High throughput, Customized annotation for sizeable regional gDNA sequence
Annotation is as its narrow sense as a set of descriptions of biologically-interesting objects/features associated with specific sequences. For example: map of SNPs, STS, gene, regulatory elements, primers/oligos, amplicons, etc.
DNannotator serves two major purposes for customized annotation:
Two major categories of annotation functions:
Annotation to user supplied gDNA sequence integrates:
Or
Annotation to Genome Browser latest freeze (Attention: Human genome only!)
Before doing analysis, be sure to understand the definitions of "annotated sequence" and "un-annotated sequence" used in this DNannotator.
Major Functions of DNannotator:
Workflow for individual function
Annotation functions:
Affiliated functions:
It's designed to do batch data processing.
Data Size limit
Currently sequence is limited to 20 Mb size. If you have longer sequence to analyze, please contact the author for special services.
You have a choice to get all output mailed to you as compressed by gzip, and you can use gunzip, a freeware, to de-compress it.
You may also want to use gzip to compress your data file before uploading it, too (BUT, Don't gzip more than one file into one file for uploading. For example, if you have 100 sequences in FASTA format to be analyzed, you have to put them into one file. Don't use gzip to compress individual files into one .gz file and upload it). With compression, you will be able to process more data. Generally, the data size can shrink to 1/3 to 1/4 the original size.
Requirement:
1) Organized input data file for both source data and target gDNA unless mapping to public assembly;
2) It's better to have an email
account big enough to accept attachment of your analysis results. If you are
using small email box like hotmail, please adjust the parameters about mail box
accordingly.
Privacy Issue and Disclaimer
All data submitted to server for analysis will not be recorded. No backup. It will be deleted automatically within 3 -7 days, depending on the server disk space usage (It has nothing to do with your own local data in your own computer). Unless the user requests investigation of bugs relating to a certain data set, no one will read the data at all. But we do keep a log of which email account used which function of DNannotator. That's the only track you will leave after you visit my server.
Even for the un-deliverable, oversized results, only the linker provided in an email (informing you about the failure of delivery and where you can get the results) could let you access the results. Nobody else can get the data without that email information.
Certainly, this is not commercial transaction facility, so, no secured data transfer (including data upload, download and email) is provided. If anybody spies on you in the path of network (as it could be done in your daily Internet life), we don't hold any responsibility.
We don't hold any responsibility of data loss, data damage or hacker attack for using this service either, thought that's our concern too, and it's very likely to occur.
If you have problems, comments, suggestions, or found bugs,
please write to Chunyu Liu