Melitaea cinxia manual annotation

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• Version 1 published in 2014
• Version 2: sequenced with PacBio

• Gene prediction software can detect the location of the genes in the genome
• Data from RNA sequencing gives signals about where there are genes in the genome 
• Automated gene prediction may give false results
  • True positives vs. false positives
  • True negatives vs. false negative

• Will go through most (if not all) of the automated gene predictions
• Trained human eyes will confirm and curate the computer-generated gene predictions
• Apollo - online collaborative annotation tool

• Annotating at least 30 genes by Wed 30/01/2019 entitles the participant co-authorship in the forthcoming genome paper
• The co-authorship only includes the person doing the actual annotation work and does not include group members, funding organizations or other stakeholders
• All annotations are curated by the coordinator / admins
• There will be a small prize for the top three annotators (based on number of genes accepted by the curators) – so you are more than welcome to annotate > 30 genes

Prerequisites

• Install either Firefox or Chrome if you do not have one of them already
  • Firefox: http://www.firefox.com/
  • Chrome: http://www.google.com/chrome

Users without University of Helsinki user account

• We are currently arranging VPN accounts for people outside the university of Helsinki to connect to the server

Users with UH account

• See that you have Pulse Secure installed (standard in UH laptops)
• If not installed you can download it from https://helpdesk.it.helsinki.fi/en/instructions/logging-and-connections/network…
• A way to connect without Pulse Secure is via the VPN portal at https://www.vpn.helsinki.fi
• Follow the instructions and select a suitable way to connect here 
• OR see that you can connect your laptop to internet via the eduroam WLAN
  • https://www.eduroam.org/about/connect-yourself

Test annotation server access

• Try URL: http://dna-marker.biocenter.helsinki.fi:8018/apollo
• If you get a login window on the center of the screen, then you already have access to the server

Selecting genes to annotate

• After you have registered, a selection of genes will be assigned to you to annotate from the predicted genes.  If you are interested in annotating a specific gene family please email daniel.blande (at) helsinki.fi with the PFAM code and we will try to allocate genes from that family.
• http://pfam.xfam.org/
• Select “KEYWORD SEARCH” and enter your assigned gene family or some suitable keyword related to the gene family

• Apollo annotation server
• Apollo demo server
  • Username: demo@demo.com
  • Password: demo

Basic annotation quick reference sheet

Details of these steps are in the basic annotation guide above

1.    You will receive a list of genes to annotate form Daniel Blande.  If you have not received a list please contact daniel.blande (at) helsinki.fi
2.    Open your received list of genes and login to main annotation server (Apollo) 
3.    Locate a gene model in Apollo from your gene list 
4.    Make relevant evidence tracks visible in the Apollo view 
5.    Add annotation to the User-created annotation area 
6.    Get the cDNA sequence of your annotation and perform BLASTX alignment  
7.    Perform multiple alignment against the best BLASTX hits 
8.    Set correct exon lengths and add missing exons into your annotation 
9.    Edit information of your annotation and move on to next gene on your list  
10.    Once you’re done with the annotations for the day, logout from Apollo 
11.    Once your whole gene list is finished and commented, send it back to daniel.blande (at) helsinki.fi . You may also request a new gene list at the same time. Select a new gene family and send a list of identifiers. 

Support available during and post-annotation at:

daniel.blande (at) helsinki.fi

juhana.kammonen (at) helsinki.fi

Slack instant messaging: https://mcinxiaannota-ctk7011.slack.com/

1. Login to the Apollo service fails. After entering username and password the browser returns to the login page

• First check that you are attempting login using either Mozilla Firefox or Google Chrome internet browser. Logins are disabled for Internet Explorer, at least IE version 11.
• If this still happens and you get message “Invalid login” on the screen after, say, three attempts of logging in, send an email to daniel.blande (at) helsinki.fi to reclaim your Apollo credentials.

2. Features such as scaffold coordinates are missing from the main annotation view

The Apollo server may be crowded during the annotation phase (there are 30+ people performing annotations). This may cause some loading of scripts to take a long time or even your browser to warn about this. Logout / re-login may help here. Apollo saves the location of your session so that when the user makes a re-login, the view and location within the genome will be the same as when logging out.

We have completed the manual annotation phase of the M. cinxia genome project.  Thank you to everyone who was involved in the annotation.  In total 1232 genes (1448 transcripts) have been annotated across a variety of gene families. 

The prize winners for completing the most annotations were Janina, Tarja and Anne.