BAC and Gene Annotator
Home
Help
ACPFG BAC and Gene Annotator Help Pages
This is a guide for using the BAC and Gene Annotator. If you can't find what you need here then please look up our FAQ
Click on a link below to view help for that topic.
Using the BAC annotator
The BAC and Gene Annotator could take some time to process your data so an email will be sent to you when the job is done. Please enter your email address at step 1 and at step 2 please choose the type of annotation, BAC and Gene.



Next you have to enter the sequences to annotate. You can upload a file or you can paste in a sequence in FASTA format. The uploaded file will also be in FASTA format.
For BAC annotation only.
Genescan can use a
number of different
parameter files for
predicting genes in
different types of
organisms. You can
change the genscan
input setting here.

Finally press start to start the pipeline.

Back To Top
Advanced options
The following section describes how to use the advanced options of the Annotator.
Click here to show or hide the advanced options.
By default the Annotator will blast against genbank and uniref. If you would like to blast against a specific reference genome you can do so here.
Here you can choose which libraries repeatmasker will use when masking the input BAC.

Back To Top
Interpreting the output
If the job is a BAC annotation the main results page will contain a graphical guide to the annotation similar to the one below. It is possible to navigate along the target sequence and view other sequences which share a high amount of similarity.
Clicking on the images will take you to a page containing more detail about the aligned sequence.
This is the navigation box. Use these buttons to navigate along the BAC
If you wish to navigate to a particular position on the BAC enter the start and end locations here.
This is the name of the BAC being annotated
Lighter sections represent areas masked by repeatmasker using the libaries you specified in Advanced options.
Predicted genes are aligned to their positions on the BAC. Clicking the gene will take you to a page with detailed information about the gene.
Blast is used to find similar positions to sequences stored in genbank or on refernece sequences. Each graphic links out to a one of a number of sites with detailed information about the aligned sequence.



If the job is a BAC annotation genscan is used to produce a set of predicted genes. The summary information is presented in a table like the one below. If the job is for annotating a set of real genes the results page will consist of this page only. Note that each gene either real or predicted has its own detailed results page.
This is a link to the page which describes the annotation of the gene in more detail This is a link to the top blast hit against uniref90 This is some more information about the top blast hit


Each gene has its own page which contains detailed information about which sequences it is similar to and any GO terms related to high scoring uniref hits.

Back To Top
Saving output
Currently there is no way to save the output of the annotation although we hope to add this functionality very soon.
All jobs will be kept on the server for 30 days before they are deleted. If you wish to keep them there longer please contact

Back To Top