Gene Family Diversity

Introduction

We use FastTree v2.1.11 to infer approximately-maximum-likelihood phylogenetic trees from alignments of protein sequences of target gene family. We outline the gene number and status of the family members to show the diversity and evolution of target gene family.

There are two modes to perform this analysis. You can begin by selecting a protein and some species (identification + diversity) or uploading the required files (diversity).

Citation

[1]Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010 Mar 10;5(3):e9490. doi: 10.1371/journal.pone.0009490. PMID: 20224823; PMCID: PMC2835736.

Module Structure

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`Please select one mode to perform this analysis.`

First Mode (identification + diversity)

Step 1 Input Data

Select a protein or paste a protein sequence as input. Click the top right Example to input an example data.

Protein name or PfamID: 19,632 analyzable proteins are from Pfam-A database. PfamID can also be used as input. The search engine supports fuzzy searches.

Do not use

Greek letters: revise as English equivalents (e.g.,PPARgamma, not PPARγ)
Roman numerals: revise as Arabic numerals (e.g., ABCG1, not ABCGI)

OR

Protein sequence: a protein sequence in fasta format. The first line begins with a greater-than (">") symbol, followed by a gene or sequence ID. Spaces are not allowed on the first line and blank lines are not allowed in the middle of FASTA input.

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Species name: select the scientific/common name of the species the sequence belongs to. The list of available species is provided on the Species page.

Step 3 Set Parameters

ProjectID(required): Set the name of this task and the result file names will start with "ProjectID".

E-value(required): Set the E-value (expectation values) threshold for saving hits of hmmer or tblastn. E-value is a statistical measure of how likely your sequence of interest could have arisen by pure chance. Default = 1e-20.

Second Mode (diversity)

Upload files

You can download the required files from the results of the Gene Family Identification analysis or prepare them by yourself.

This analysis requires two files:

Protein sequences of gene family members in FASTA (fa) format (one file per species)
Feature information of gene family members (.txt)

File Description

Protein sequences(required): Protein sequence of gene family members in FASTA (fa) format (one file per species)

The rule for naming FASTA files of each species: species scientific name+common name.fa, e.g. HomosapiensHuman.fa The scientific/common name needs to be consistent with the name in the Species page.
FASTA format.

Feature information(required):

Please name the file: Feature.all.txt.
The first row should include the following five headers in order: Species, Protein_ID, mRNA_ID, Gene_ID, and Gene_symbol.
The first column should be the species scientific/common name consistent with the Protein sequences file name.
IDs of the second to fourth columns are ENSAMBLE IDs.
The input file is a tab-delimited text file (.txt or .tsv)
All species information is written in one file.

Results

Visualization

Overview of target gene family plot avatar