Welcome to OrthoSelect

OrthoSelect

Orthologs in Phylogenomics!

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View ortholog groups.

Useful Links

View the documentation for this page here
or get to know OrthoSelect by taking a look at theTutorial

Tutorial Section

The main goal of this tutorial is to make the user familiar with using the web interface of OrthoSelect.
Simply go through the page as it resembles a typical analysis
You will also be able to browse the results of this tutorial in section Results.
Input

Fasta Files
Input Settings
Sequence Upload
Check Parameters & Start Analysis

Results

Overview
Functional Classification
Taxa/Gene table
Annotations
Ortholog Groups
Download

Index

Fasta Files

5 different species were selected for the test dataset.Sequences were downloaded from JGI.
Based on those sequences, a test dataset has been generated using only a small subset of sequences mapping to a small subset of ortholog groups. This was done intentionally to provide a test dataset for this tutorial.
The species are listed in the table below (Sequences can be downloaded here).

Taxon	File name	Type of Sequence
Aspergillus niger	Aspni1 FilteredModels1.na.fasta	Transcripts
Ciona intestinalis	Cintestinals EST clusters.fasta	ESTs
Daphnia pulex	FrozenGeneCatalog 2007 07 03.na.fasta	Transcripts
Lottia gigantea	Lotgi1 EstClusters na....fasta	ESTs
Monosiga brevicollis	Monbr1 ESTclusters.fasta	ESTs

Make sure that all sequences have a correct fasta header.
(If you want to convert fasta header intothe correct format, you can use the header converter)
Click

here to view the fasta headers.
Hide

Index

Input Settings

To start the analysis, go here and enter name and email address to which results will be sent.

Select the expert options

and change the expectation value for the initial BLAST-searches.
Select an expectation value of 1e-20 and require the translated sequence to be at least 30 amino acids in length.
Leaving the other parameters unchanged, proceed to the sequence upload page by clicking "Upload Sequence".

Index

Sequence Upload

Upload our sequences using the browse and upload button.
After successfully uploading all sequence we see the following table.

Change the names OrthoSelect uses for each species throughout the analysis. Click "Name association" and enter the following

We finish the upload of sequences by clicking "Check Parameters & Start".

Index

Check Parameters & Start Analysis

The next windows gives an overview of the selected parameters and uploaded sequences.

To make changes, we can always use the navigation bar.

Start the analysis by clicking "start analysis".

Index

Results

The following page appears after receiving an email.
Click the following link to browse pre-calculated results : Results

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Functional Classification

The first thing is a short overview about the diversity of our sequences. For this, we take a look an overview of the assigned functional classes by clicking the statistics link.

Most sequences belong to the group of post transitional modification, protein turnover, chaperones. 10 sequences were assigned to as belonging to signal transduction mechanisms, 8 belonging to RNA processing and modification, and 6 to Translation, ribosomal structure and biogenesis.

Index

Taxa/Gene Table

We click on "View table for all ortholog groups" to first look at all ortholog groups to which sequences have been assigned. Even those containing only one sequence in total.

Most sequences have been assigned to OG KOG0019. Aspergillus niger does not have a sequence present for OGs KOG0003 (Ubiquitin/60s ribosomal protein L40 fusion) and KOG0004 (Ubiquitin/40S ribosomal protein S27a fusion).
This table is a valuable resource when deciding which genes to further consider in the analysis.

We go back to the main results section by clicking "Results overview"

After getting an overview about the composition of the uploaded sequences, take a closer look, first on the annotations for a single species and then on a single ortholog group.

Index

Annotations

Looking at the annotations page for "Ciona intestinalis"

we find that 10 out of 12 sequences could be assigned to an ortholog group. We also see to which ortholog groups sequences from this species have been assigned (KOG0003, ...,KOG0213).
The statistics section shows that the majority of sequences (10/12) could be assigned to an OG. This means that a high percentage of the sequences from Ciona intestinalis has potential orthologs.

It also show us that most of the sequences have been annotated as belonging to "Posttranslational modification, protein turnover, chaperones".

Index

Ortholog Groups

The ortholog groups can be selected by clicking the "Ortholog groups" link in the navigation bar. The following page provides an overview of how many sequences have been assigned to ortholog group:

Take a closer look at one of the ortholog groups now. Select the OG "KOG0027" under "Ortholog Groups".
You see the following page

10 Sequences from 5 different species have been assigned to this group.
The pie chart gives us information from which taxa sequences have been assigned to this group.
You can now view/download different sequences:
Clicking the link "View Seqs." takes us to page showing different files for this OG. These files include:
(A) All sequences assigned to this group (nucleotides, unaligned)
(B) All sequences assigned to this group (proteins, unaligned)
(C) The alignment were the most probable ortholog/species has been selected
(D) same as (C), but with eliminated poorly aligned regions using Gblocks
(E) same as (D), but without sequences that are too short (according to given threshold)
We can either view/download the plain text files by clicking the download link or view them using jalview.

Index

Download

Now that you have thoroughly investigated the results of our analysis, you want to download the results to further process your data.

We do this by clicking the download link from the navigation bar. The downloaded zip-archive can then be extracted. The directory structure is described in the user guide