b) What is needed is the comparison of RNAseq data to peptide (mass spec) sequencing.
For example, JIC and the Institute for Food Research, which is conveniently located just over the road, share a proteomics facility that is equipped with mass spec and protein sequencing machinery.
In the top-down approach, the histone proteoforms are delivered to the mass spec intact and then sequenced by fragmentation inside the instrument, thereby retaining the critical linkage data.
A 14 amino acid DBP-maf peptide was synthesized (Ana Spec, Fremont,CA) with the amino acid sequence: Ac-TPTELAKLVNKRS E Ac-TPTELAKLVNKRS E
One different allele was found for each of the following gene sequences: spd1 (among 6 strains), speC (among 6 strains), and speL (among 4 strains).
The enzymes in the fourth building block, spe1 from S. cerevisiae and speC, speF from E. coli, have very dissimilar sequences (E-value > 100).
A log-likelihood score distribution for each PSSM was determined using the sequence scoring feature of the ANN-Spec tool (Workman and Stormo, 2000) over all possible sites in the yeast genome.
The mutant was then confirmed by polymerase chain reaction (PCR) and sequencing of the junction site of the Spec cassette as described previously [ 20].
As in MGAS9249 and MGAS2096 (two previously sequenced emm12 genomes), HKU16 also possesses the speC and spd1 genes, but the superantigen gene ssa is present in HKU16 and not in the other two genomes.
We identified speA, speC, speG, speH, speI, speJ, speM, ssa, and smeZ gene sequences from at least one isolate.
Although spe1, speC and speF are non-homologous, lysA (EC: 4.1.1.20) in E. coli has a sequence similar to that of spe1 (E-value = 2.5 × 10-7).
