How to Generate a Dataset of Homologous Sequences?

Preparing a list of homologues involves identifying and collecting protein sequences that are evolutionarily related and share a common ancestor. Here are some general steps that can be followed to prepare a list of homologues:

Determine the protein of interest: Identify the protein of interest for which you want to find homologues. This protein should be well-characterized and have a known function. Tools to Generate Homologues Dataset

Perform a sequence search: Use a sequence search tool, such as BLAST or PSI-BLAST, to search for sequences that are similar to the protein of interest. These tools compare the protein sequence against a database of known protein sequences and return a list of hits that have significant sequence similarity.

Filter the hits: The sequence search may return a large number of hits, many of which may be irrelevant or redundant. To filter the hits, you can set a threshold for sequence similarities, such as a minimum percentage identity or a minimum e-value. You can also use tools such as CD-HIT or ClustalW to cluster similar sequences and remove redundant hits.

Verify the hits: Once you have a list of hits, you can verify that they are indeed homologues of the protein of interest. This can be done by comparing the sequences and checking for conserved domains, motifs, and other features that are characteristic of the protein family. You can also use phylogenetic analysis tools, such as MEGA or PhyloT, to construct a tree of the protein sequences and visualize their evolutionary relationships.

Refine the list: Depending on the research question and the purpose of the homologue list, you may need to further refine the list by removing sequences that are too divergent or too similar, or by including sequences from specific taxa or environments.

Overall, preparing a list of homologues requires a combination of bioinformatics tools and manual curation to identify and collect protein sequences that are evolutionarily related and share a common ancestor with the protein of interest.