Comparison of SR protein families in eukaryotes

The referenced paper[2] also included gene sequences for all known members of the SR protein group, rendering a comparison of members possible. There were two possible ways to compare the group after extracting the data and joining them into a FASTA file: The first was to compare the protein sequence of each group member with the protein sequence of the same member in each provided species to get an impression how the specific protein evolved. Another possible inquiry was the comparison of all group members in one species to compare the proteins themselves.
In each case the procedure was the same:

1.

Create FASTA files from supplemental material[3]

2.

Run ClustalW on FASTA file to align the sequences e.g. clustal p54/p54.fas

3.

Run t_coffee on the created alignment to get better results e.g. t_coffee p54/p54.aln -outfile p54/p54.tc.aln

4.

Extract the information from the N-J-tree taken from t_coffee e.g. njplot.linux p54/p54.phb

Now that the basic structure of specific SR and SR-related proteins was presented, it's reasonable to align the different groups of proteins. By this, it's possible to compare all known protein sequences of each groups in one species against proteins of the same group in other species. After doing so, an alignment of all SR proteins in human against each other is performed, too.

This research was done based on the following FASTA files:

1. SRp20 9G8: assets/9G8-SRp20.fas
2. p54 SRp86: assets/p54.fas
3. RY1: assets/RY1.fas
4. SC35: assets/SC35.fas
5. SRm300: assets/SRm300.fas
6. SRp30c-ASF: assets/SRp30c-ASF.fas
7. SRp40-55-75: assets/SRp40-55-75.fas
8. TopoI-B: assets/TopoI-B.fas
9. Tra2: assets/Tra2.fas
10. Comparison of all SR proteins in human: assets/comp_human.fas