A k-mer refers to all possible subsequences of length k in a DNA sequence, RNA sequence or amino acid sequence. Figure 3 shows the process of examining a k-mer in a sliding window mode in a sequence when k is three, in which there are 21 3-mers, namely, GCC, CCA, CAA, AAC, AC...
mRNAs for secreted enzymes encode an ER-localizing signal peptide consisting of about several dozen amino acid residues. When this sequence is translated in the cytoplasm, SRP binds to the ER-localized signal peptide and prevents translation elongation by the ribosome. mRNAs encoding secreted enzymes ...
crescentus by utilizing the online tool version of the TAI calculator (Sabi et al., 2017). C. crescentus was selected as the organism, and a FASTA file was uploaded with sequences of all of C. crescentus protein coding genes. stAIcalc (Sabi et al., 2017) calculated a TAI value for ...
As the identification of transcripts involved immature mRNA fragments, we used four tools, namely Coding Potential Calculator (CPC), Pfam-scan (PFAM), phylogenetic codon substitution fre- quency (phyloCSF), Coding-Non-Coding-Index (CNCI) to remove potential coding transcripts. Finally, 2805 putative...
The E-EL-H1584 detects survivin-wild-type protein (isoform 1, Baculoviral IAP repeat-containing protein 5, length 142, also known as alpha, apoptosis inhibitor 4, or apoptosis inhibitor survivin) (UniParc, identifier: O15392-1), chosen as the canonical sequence (eLabscience Biotechnology, ...
The amino acid sequences of these POIs were scanned for DnaK binding sequence using Limbo [38] and predicted for the possible disulfide formation using DISULFIND [39]. Since DnaK and DnaJ share the majority of binding sites in E. coli [40], this analysis can be used to assess the ...
1.2.4 [62], the coding potential calculator 2 (CPC2) v. 2.0.1 [63], the flexible extraction of lncRNAs (Feelnc) [64], and the predictor of lncRNAs and mRNAs based on an improved k-mer scheme (PLEK) v. 0.2 [65]. Simultaneously, transcripts' sequences were aligned into the protein ...
(E) Sequence of the predicted SVR. The 5′ RACE sequences are indicated in yellow, and 3′ RACE sequences are not indicated for the same to RNA-Seq sequences. The 5′ NGSP (nested gene specific primer) and GSP (gene specific primer) are indicated in blue, the 3′ NGSP and GSP ...