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Supplementary materials to: |
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This is part 3 of a series of articles on the issue of sequence similarity and homology, especially in compositionally biased sequences. The two preceding articles are accessible via these links: part 1 and part 2.
Full reference
Biology Direct, 6(57), doi:10.1186/1745-6150-6-57
Supplementary Tables
Supplementary to methods and materials
Below, we provide summary of seven datasets (functional TMs SCOP/UniProt-derived, membrane anchors, signal anchors, functional alpha-helices, signal peptides, low-complexity segments) that were used to compute our results.
Each summary contains the sequence ids, segment ids, TM positions, TM sequence and the functional motif (when available) of the relevant entries.
- Summary of functional TMs (SCOP-derived, 984 entries, 61kB) click here
- Summary of functional TMs (UniProt-derived, 3923 entries, 224kB) click here
- Summary of membrane anchors (378 entries, 19kB) click here
- Summary of signal anchors (2280 entries, 109kB) click here
- Summary of functional alpha-helices (17193 entries, 990kB) click here
- Summary of signal peptides (1664 entries, 83kB) click here
- Summary of low-complexity segments (577373 entries, 53MB) click here
For use in this work, these datasets have been modified for the suppression of redundancy. Note that cd-hit (options -n 5 -c 1) is to be applied for the removal of sub-strings and repeats of TM helices in each set prior to the computations of the error rates (i.e., true-negative rates & false-positive rates). The final form of the datasets is provided below.
- Final set of functional TMs (SCOP-derived, 83 entries, 4kB) click here
- Final set of functional TMs (UniProt-derived, 1741 entries, 73kB) click here
- Final set of membrane anchors (303 entries, 13kB) click here
- Final set of signal anchors (1767 entries, 76kB) click here
- Final set of functional alpha-helices (1330 entries, 56kB) click here
- Final set of signal peptides (262 entries, 12kB) click here
- Final set of low-complexity segments (475207 entries, 42MB) click here
Supplementary to the analysis of the single-spanning membrane proteins
Below, we provide the results of the full-length and TM-only segment for the sequence entries in the disease-related proteins & immune receptors.
For details of the entries, refer to "Moore et.al., 2008, Structure, v16, pp991-1001"
All files are compressed (1) by WinRAR, (2) in the ".tar.gz" format and (3) by ".zip"ping.
Supplementary to the analysis of the multi-spanning membrane proteins
Below, we provide the masked pattern/ratio of the 326 TCDB families (2202 protein sequences). In addition, the error rates of the TCDB sequences which are compiled
from the BlastP results of the corresponding original/masked/control sequences are also provided. Note that each set of results are computed
for the z-score threshold of f=0.84, 1.0, 1.282, 1.645, 1.98 respectively.
- Summary of 326 TCDB families click here. The description of the file format is available here.
- Mask ratios/pattern and error rates (f=0.84; download)
- Mask ratios/pattern and error rates (f=1.0; download)
- Mask ratios/pattern and error rates (f=1.282; download)
- Mask ratios/pattern and error rates (f=1.645; download)
- Mask ratios/pattern and error rates (f=1.98; download)
TMSOC (TM Simple or Complex) program
Below, we provide the program (written as PERL modules) that calculates the complexity, hydrophobicity and z-score of TM segments.
The program requires the (1) protein sequence and (2) TM range(s) as inputs.
- download the program as zip-archive here
For windows OS, we recommend WinRAR for unzipping.
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