ESG: Extended Similarity Group Job Submission

Download ESG Tutorial

Cite:
Meghana Chitale, Troy Hawkins, Changsoon Park, & Daisuke Kihara ESG: Extended similarity group method for automated protein function prediction, Bioinformatics, 25: 1739-1745(2009).


Related Articles:
Meghana Chitale*, Ishita K. Khan*, & Daisuke Kihara (* equal contribution), In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment. BMC Bioinformatics, 14 Suppl 3: S2 (2013),

Ishita Khan, Meghana Chitale, Catherine Rayon, & Daisuke Kihara, Evaluation of function predictions by PFP, ESG,and PSI-BLAST for moonlighting proteins. BMC Proceedings, 6 Suppl 7: S5 (2012),

Meghana Chitale & Daisuke Kihara , Enhanced sequence-based function prediction methods and application to functional similairty networks., Protein function prediction for omics era, D. Kihara ed., Chapter 2, pp. 19-34, Springer.(2011),

Lee Sael*, Meghana Chitale*, & Daisuke Kihara (* equal contribution), Structure- and sequence-based function prediction for non-homologous proteins. Journal of Structural and Functional Genomics, 13: 111-123 (2012)

Tutorial

For any questions regarding ESG contact the administration at info@kiharalab.org

This method allows user to submit protein sequence(s) and obtain annotation prediction for the sequence(s) in terms of Gene Ontology terms. The underlying ESG algorithm can be found here . To learn more about each input you can click on the question mark next to it.

Part1: Steps for submitting job as anonymous user

1. Go to http://www.kiharalab.org/web/software.php . To start a new job click on the ESG logo highlighted in red below. This will open ESG job submission page in your browser.

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2. You can enter one or more query protein sequence(s) in fasta format in the text box titled "Enter Query Sequence(s)".
Example of an input sequence:

>tr|Q99ML3|Q99ML3_MOU
AAPYLKTKFICVTPTTCSNTIDLPMSPRTLDSLMQFGNNGEGAEPSAGGQF

You can also click on “Load Sample” link to load this sequence in the text box and follow the next steps. Clicking on “Clear” link will clear the text box for sequence and load default ESG parameters in the boxes below.

Or you can click on browse/choose file button and upload a fasta file containing query sequences. Currently we support maximum 10 query sequences in one job.

To clear sequence, click on "Clear" link above the protein sequence text box.


3. Choose ESG parameters

“Number of hits” indicates number of PSI-BLAST hits to be considered at each level of ESG. Default value of this parameter is 10. “Number of stages” indicates the levels of neighborhood around the query protein that will be considered by ESG. Default value for this parameter is 2. Due to computational constraints currently we support parameters where {Number of hits^ (Number of stages-1)} does not exceed 100. Details about the parameters can be found in the original paper.

4. When you submit a job without logging in, you can bookmark the results URL and refer back to the job result. Registration to the website provides you additional features, including receiving email notifications about your jobs, viewing the progress status, and manage your jobs in a table.

5. After loading the query sequence(s) click on the Submit button. This will take you to the Your Job page and shows the status of your jobs.

When your job is complete, predicted Gene Ontology terms for the query protein will be displayed. Or you can refresh the page to go to results. The results page will show ESG input parameters, query sequence and prediction terms for each Gene Ontology category (Molecular function, Biological Process and Cellular Component) that have probability greater than 5%. The results page will also provide link to the results in xml format which you can download for further processing. Clicking the plus button next to a GO term will show a list of BLAST hit sequences that contributed scores to the GO term. The percentage next to each sequence ID shows the the percentage of the score that originates from the sequence in the total score assigned to the GO term.

If you click "Download Prediction's XML", an XML file that have all information shown in the result page can be obtained. Clicking "Visualization of Predicted GO Terms" will pop up a new window that visualizes the predicted GO terms in the GO graph. The tutorial of the GO visualizer is available here . Below the redirect link, there are three links of downloading static image of visualization. Once clicked it, the server will render the SVG image for the user and display it on the web page. At the top of static image, there is a download link to download the PNG image file and user can also save the SVG by saving the static page. (After openning the page, please wait some time to allow server to generate those file.)

6. If you close your browser and need to go back to your job results then you can use the “Job Retrieval” text box on the right side of the web page. It has been highlighted in red in the screenshot below. When you enter a valid job ID and click on “Fetch Job”, you will see the job status or results page depending on if the job is complete or not.

Part2: Steps for logging in and submitting ESG job

1. Open ESG job submission page in your browser.

2. Click on the “Register” link on the right side of the page, it is highlighted in red in the screenshot above. It will take you to the account creation page shown below.

Click on the “Forgot Password” link on the right side of the page. It will take you to the password reset page. After entering the correct email, you will receive a link to reset your password.

Here you should enter your username and password information. The email address is optional; you should enter it if you wish to receive email notifications about your job status. If you don’t check the “Receive Email Notification” check box you will have to log in to the server and check the status of your jobs.


3. Once you have your account set up you can log in and submit jobs for processing. Enter your username and password in the text boxes provided on the right side of the web page and click login. This will redirect you to the software page with links to your jobs appears on right side frame on the page.

To start a new job click on "PFP Submission" link under Job Submission on the top of the right bar.

This will direct you to the ESG job submission page shown in step 1.

4. You can enter one or more query protein sequence(s) in fasta format in the text box titled “Enter Query Sequence(s)”.
Example of an input sequence:

>tr|Q99ML3|Q99ML3_MOU
AAPYLKTKFICVTPTTCSNTIDLPMSPRTLDSLMQFGNNGEGAEPSAGGQF

You can also click on “Load Sample” link to load this sequence in the text box and follow the next steps. Clicking on “Clear” link will clear the text box for sequence and load default ESG parameters in the boxes below.

Or you can click on browse button and upload a fasta file that contains query sequences.
Currently we support maximum 10 query sequences in one job.

5. Choose ESG parameters
“Number of hits” indicates number of PSI-BLAST hits to be considered at each level of ESG. Default value of this parameter is 10. “Number of stages” indicates the levels of neighborhood around the query protein that will be considered by ESG. Default value for this parameter is 2. Due to computational constraints currently we support parameters where {Number of hits^ (Number of stages-1)} does not exceed 100. Details about the parameters can be found in the original paper.

6. After loading the query sequence(s) and parameters click on submit button. This will take you to the results page and show your job waiting for processing. You can log in again later to check the status of your job and access the results when it is complete. You can also enter job id in “Job Retrieval” text box on right side of the page and click “Fetch Job” to view the status of job and results. If you have chosen to get email notifications in your account settings then you will be notified by an email when your job is complete.

7. When you job status shows complete, click on the job ID to view predicted Gene Ontology terms for the query protein. The results page will also provide link to the results in xml format which you can download for further processing.

Part3: Steps for submitting a batch job using ESG

1. Open ESG job submission page in your browser.

2. You can enter more than one query protein sequences in fasta format in the text box titled “Enter Query Sequence(s)”.
Consider the following sequences that you can enter.


>sp|P56851|EP3B_HUMAN
MASSLKIWGTLLALLCILCTLLVQSKEVSWREFMKQHYLSPSREFREYKCDVLMRENEAL
KDKSSHMFIYISWYKIEHICTSDNWMDRFRNAYVWVQNPLKVLKCHQENSKNSYTESRSF
NYIEFHCSMDGYVDSIEDLKMVEPIGN
>sp|P13811|ELBH_ECOLX
MNKVKFYVLFTALLSSLCAHGAPQSITELCSEYHNTQIYTINDKILSYTESMAGKREMVI
ITFKSGATFQVEVPGSQHIDSQKKAIERMKDTLRITYLTETKIDKLCVWNNKTPNSIAAI
SMEN
>sp|P05928|VPR_HV1BR
MEQAPEDQGPQREPHNEWTLELLEELKNEAVRHFPRIWLHGLGQHIYETYGDTWAGVEAI
IRILQQLLFIHFRIGCRHSRIGVTQQRRARNGASRS


Or you can click on browse button and upload a fasta file containing query sequences. Currently we support maximum 10 query sequences in one job.


3. Follow steps 3 to 6 from part 1 if you are submitting the job as anonymous or steps 5 to 7 from part 2 if you are logged in as a registered user. On the job status page the job type will be shown as batch.

Once the processing is complete the results will be displayed in the table with each sequence, its identifier and a clickable link which will take you to detailed results for that sequence.