Frodo's quest is the main focus, and Aragorn is the main sub-plot, and many sequences (such as Tom Bombadil) that do not contribute directly to those two plots were left out.
Although researchers have been able to identify the roles of many sequences, such as ribosomal and protein-coding RNAs, they have had to classify a substantial number of the newly discovered transcripts as TUFs (transcripts of unknown function).
Many biological sequences such as genomic sequences contain many long repeats and are especially prone to long common prefixes.
This is more likely to be found in large genomes, as they usually contain many repetitive sequences, such as transposable elements [ 37, 45].
This can be explained at least in part by the fact that there are not so many repeated sequences, such as Ty elements (1.8%), in the total yeast chromosome as in the mammalian genome (Krebs et al. 2009).
(3) Although a web-server for Euk-mPLoc has been established at http://www.csbio.sjtu.edu.cn/bioinf/euk-multi-2/, only one query protein sequence at a time is allowed when using the web-server to conduct prediction; for the convenience of users in handling many query protein sequences, such a rigid limit should be improved.
In many sequences in databases such as GenBank, only the genes within cassettes, rather than whole cassettes, are annotated and the same gene/cassette may be given different names in different entries, hampering analysis.
Ingolia et al. (Cell Rep., September 2014), argue that translation on transcripts outside of protein-coding regions can in fact produce polypeptides and therefore a TE value is valid for many non-coding sequences such as 5'UTRs or lncRNAs.
For many sequences of random variables, such as independent sequence, negatively associated sequence (see Shao [18]), negatively dependent sequence (see Asadian et al. [19]), ρ ∗ -mixing sequence (see Utev and Peligrad [20]), φ-mixing sequence (see Wang et al. [21]) and so forth, the Kolmogorov type inequality also holds.
It is noted that many of these target sequences, such as the target of miR-125 in HBV, the targets of miR-448 and miR-122 in HCV (Li et al., 2011; Pedersen et al., 2007; Potenza et al., 2011), were found well conserved through viral genomes, and several of them have been preferentially exploited for new anti-viral strategies (Russo and Potenza, 2011).
Building consensus trees from bootstrap pseudoreplicates of an alignment can minimize the impact of ties, though in instances where there are many very closely related sequences such as in the case of tuna, ties can still be problematic [86].
