AMPK Methods and Protocols
Likewise, you can also apply a cutoff for the minimal FAS score (default is 0). This option serves to reduce the impact of orth ...
Align the orthologous sequences with MUSCLE [32](see Note 12) and store the alignment in the appropriate file for- mat. Most tr ...
In cases where the alignment contains lots of gaps, you can add an optional post-processing step with Guidance [40] or TCS [41] ...
–f A –N 100 –p 77 –x 933. Here, we use the LG model of protein sequence evolution [42] with empirical equilibrium frequencies fo ...
duplicated gene (Fig.10d). If gene loss appears prevalent in one subtree, it is worthwhile considering a tree reconstruction art ...
Use then the Shimodaira–Hasegawa test [44] implemented into RAxML to test whether the ML tree explains the data significantly b ...
3.8 Integration of Sequence Phylogeny and Domain Architecture You will obtain a phylogenetic tree resembling the evolutionary hi ...
PK PK PK PK PK PK PK PK PK PK PK PK PK PK PK PK PK PK PK PK PK PK PK PK PK PK PK PH PK PKC C1 C1C1C1 C2C1C 1 PK PKC C1 C1C1C1 C2 ...
In a nutshell, a gene missed in the annotation of a draft genome does little harm to the analysis, if there is a second genome ...
now further that for the same protein, you then don’t find any orthologs in nonmammalian eukaryotes, but there are few bacterial ...
Reconstructing the evolutionary history of old proteins that extends easily over a billion years or more is tricky, as the phyl ...
Jensen RA (2001) Orthologs and paralogs - we need to get it right. Genome Biol 2(8):inter- actions1002.1–interactions1002.3. ht ...
Koestler T, von Haeseler A, Ebersberger I (2010) FACT: functional annotation transfer between proteins with similar feature arc ...
Chapter 9 AMPK Protein Interaction Analyses by Yeast Two-Hybrid Pascual Sanz, Rosa Viana, and Maria Adelaida Garcia-Gimeno Abstr ...
AMPK downstream targets. Several physical protein-protein inter- action techniques (multidimensional substrate-screen, affinity ...
the additional plasmid has to be introduced into the cells containing already the bait and prey plasmids, and the new transforma ...
acid mix (9.5 g/l amino acid mix, as above), 400μl of 100 mg/ ml ampicillin, 400μl of 1 M thiamine-HCl, 800μlof1M MgSO 4 and 40μ ...
3 Methods 3.1 Transformation of Yeast Cells with Bait and Prey Plasmids and Selection of Putative Positive Transformants THY-AP ...
3.2 Qualitative β-Galactosidase Assay The technique consists basically in transferring colonies to a nitro- cellulose membrane a ...
Fig. 3Qualitative assays for two-hybrid interaction. (a) Qualitativeβ-galactosidase assay. Transformants containing different co ...
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