ConPred

[…] set at zero to return the location of all aataaa and attaaa consensus signals, along with an associated score between 0 and 1. signal peptide search (signalp 3.0) and transmembrane prediction (conpred ii) of the deduced proteins were performed online., the level of dna identity between the kozak's consensus sequence (gccgccrccatgg, r = a/g) () and the flanking 13-nucleotides around […]

[…] of the original algorithm locating tm segments in queries is preserved (sensitivity of ~95% among documented proteins with helical tm regions). in 2003, xia and colleagues presented a new approach, conpred_elite , that can predict the whole topology with accuracies of 98% for prokaryotic and 95% for eukaryotic proteins as they reported., besides the tm helix, another tm segments type […]

[…] of the full-length sequences of gpcrs with that only based on the intracellular part as adopted by other researches, we predicted the transmembrane helices of these gpcrs with the programs conpred ii and hmmtop 2.0 , then extracted the intracellular sequences and converted them into fixed-length feature vectors with the same method. the prediction results with k = 2 and k = 3 […]

[…] for all procedures involving animals., recombinant gt2 (rgt2) was produced as the large extracellular domain (animo acids 23–247) from methanobrevibacter ruminantium m1 (mru_2175) predicted using conpred ii. the dna coding for the extracellular domain was synthesized (geneart; life technologies, usa) using escherichia coli codon preference and subcloned into pet-32a (novagen, usa) to create […]

[…] the topology of oatp1b1 was predicted using the online prediction programs topcons [], phobius [], tmpred [], toppred ii [], membrain [], phdhtm [], split 4.0 [], philius [], hmmtop [], svmtm [], conpred ii [], sosui [], tmhmm [], tseg [], pred-tmr [], and memsat3 []. a homology model was generated using the protein homology/analogy recognition engine v 2.0 (phyre2) [], which modeled […]

[…] sensitive database searching using hidden markov models (hmm) was performed using the program hmmer (http://hmmer.janelia.org/) []., all obtained predicted proteins were analyzed with the tmhmm, conpred ii and hmmtop algorithms [-] to test for the typical 7-transmembrane domain topology. for those few proteins exhibiting less than seven transmembrane domains, the respective encoding gene […]