What is MEGANTE?

MEGANTE is an easy-to-use web service for integrated genome annotation. It has a simple interface to submit query sequences and performs genome annotation including repeat masking, transcript and protein alignments, computational gene prediction, similarity searches to known proteins, functional domain searches, and assignment of GO terms to the predicted genes. Multiple lines of evidence for the predictions are integrated, and an appropriate consensus exon-intron structure is selected for each locus. MEGANTE provides the results of the annotation in Microsoft Excel format and a graphical view based on a widely used genome browser, GBrowse. All data including the query sequences and annotation results are stored at the server end, enabling users to access their own data virtually from anywhere through web access.

What species does MEGANTE support?

Currently, MEGANTE can accept genome sequences of 31 species in 10 families of plants as follows:

Create an account

MEGANTE stores users' query sequences and analysis results on the server side, so that it is required to create an account at the first use.

Go to https://megante.dna.affrc.go.jp/signup, and submit your email address and a password at the form. Then we will send a confirmation email to the address you entered. Just click a link in the email to activate your account.

Upload sequences

1. Sign in to MEGANTE at https://megante.dna.affrc.go.jp/sigin.
2. Click the Upload sequence button to go to the Upload page.
3. Enter a DNA sequence or upload a file in FASTA format. Multiple sequences can be acceptable in multi-FASTA format. Each sequence is limited to up to 10 Mb, and a maximum of 100 sequences can be stored on the server.
4. Select species for the query sequence in the Select species drop-down list.
5. Turn on the Email notification check box if you need an email at the end of annotation.
6. Enter a description to identify the query in the Query name field. This is optional.
7. Click the Submit button

After submitting a query, you are redirected to the List of sequences page. You can see the states of your uploaded sequences at the page. The initial state is waiting, which means the sequence is placed into a queue, and the state is changed to running when the system starts annotation process. It takes at least 90 minutes to complete genome annotation for a 1 Mb sequence.

Get annotation results

When annotation is completed, the state will be changed to finished, and and icon will appear in the List of sequences page. Click the buttons to download or visualize annotation results, respectively.

MEGANTE predicts two classes of genes as follows:

1. Genes supported by ESTs or cDNAs

At first, a consensus gene strucutre is generated from multiple evidences, such as ab initio gene prediction, protein alignment and interspecies full-length cDNA alignment, and then the structure is merged with intraspecies EST or full-length cDNA alignments to improve accuracy.

2. Genes without transcript evidences

This class is same as (1) except that there is inconsistency between the consensus gene structure and transcript (EST or cDNA) alignments, or there are no transcript hits to the gene.

Class 1 genes are considered to be more accurate than class 2.

Manage your account

1. Sign in to MEGANTE at https://megante.dna.affrc.go.jp/sigin.
2. Click your email address in the top-right of any page to open the drop-down list.
3. Select one (change email address, change password, or delete account) in the menu.

Examples of annotation results

After finishing annotation process, users can download the analysis result as a single ZIP file, which contains ORF sequences in FASTA format, and gene structure and function information in Excel format. The web service also provides a graphical view based on GBrowse. You can see the sample results (annotation of 1 Mb in Arabidopsis chromosome 1) at the following links:

• Download annotation in ZIP format
• View annotation on genome browser

DNA and protein sequences

Analysis tools for genome annotation

Citing MEGANTE

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