1. Summary
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BOCTOPUS method takes amino acid sequence as an input and predicts the topology of the putative Transmembrane beta barrel protein. Topology refers to the number of beta strands and in and out loop location. The prediction takes into account the per-residue preferance (using separate SVMs for membrane(M), inner loop (i) and outer loop (o)) and then employs a Hidden markov model (HMM) to predict the overall topology. BOCTOPUS is based on a method previously described by us for Helical membrane proteins.
Note that the server does not predict cleavable signal peptides, which are easily confused with TM segments. If signal peptides are likely to be present in the input data, a separate signal peptide predictor such as SignalP should first be applied and predicted signal peptides cleaved off before submitting the sequence to BOCTOPUS.
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2. Usage
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This server is appropriate for topology predictions of putative transmembrane beta barrel proteins. Input to the server is amino acid sequences in FASTA format. The current version of BOCTOPUS is ideal for 1 protein sequence per input. If more than 1 input sequences are input then only the first sequence is processed. We are currently working on a faster version of BOCTOPUS for multi-sequence input.
Example input:
>1qj8A:A|PDBID|CHAIN|SEQUENCE
ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKN
QYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKNDTSDYGFSYGAGLQFNPMEN
VALDFSYEQSRIRSVDVGTWIAGVGYRF
>1TLY:B|PDBID|CHAIN|SEQUENCE
AENDKPQYLSDWWHQSVNVVGSYHTRFGPQIRNDTYLEYEAFAKKDWFDFYGYADAPVFF
GGNSDAKGIWNHGSPLFMEIEPRFSIDKLTNTDLSFGPFKEWYFANNYIYDMGRNKDGRQ
STWYMGLGTDIDTGLPMSLSMNVYAKYQWQNYGAANENEWDGYRFKIKYFVPITDLWGGQ
LSYIGFTNFDWGSDLGDDSGNAINGIKTRTNNSIASSHILALNYDHWHYSVVARYWHDGG
QWNDDAELNFGNGNFNVRSTGWGGYLVVGYNFHHHHHH
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3. Output
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The server outputs prediction results in one text file and also generates a graphical representation of the predicted topology and svm probabilitiess:
Predicted topologies (topologies.txt): Text file containing the predicted topologies for the input protein, where i=inside (cytosolic side), M=membrane and o=outside (extra-cellular side).
Graphical output (topologies.png): A graphical representation of predicted topology and svm probabilities. For representation purpose of the overall topology, M is assigned a value 2, i and o are assigned 1.8 and 2.2, respectively. Green, gray and blue lines represent the per-residue preferance to be in M,i,o.
Input sequence (inputsequence.txt): input amino acid sequence.
Profile (profile.txt): Profile comprising of SVM outputs that is then used as an input to the HMM.
PSSM (pssm.txt): Position specific scoring matrix generated for the input sequence.
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4. References
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OCTOPUS:
OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Håkan Viklund and Arne Elofsson (2008) Bioinformatics 24(15), 1662-1668. [Pubmed]
BOCTOPUS:
BOCTOPUS: Improved topology prediction of transmembrane beta barrel proteins. Sikander Hayat and Arne Elofsson Bioinformatics (Accepted 2012) [Pubmed]
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5. Contact
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