For such twilight zone of alignments, various useful strategies have been developed to get reliable alignments.
Instead of alignments, various descriptors are extracted from each sequence (e.g., amino acid composition, dipeptide frequencies, and physico-chemical properties), and pattern recognition or multivariate statistical methods are trained to discriminate positive protein samples from negative samples.
It has, however, been shown that known regulatory elements are not always correctly aligned (Siggia, 2005), an issue that is further complicated by the different alignments produced by various alignment programs (Pollard et al., 2004).
Sequence alignment has various applications like identifying homologous proteins, analyzing gene expressions and mapping variations between individuals.
We compare the energy efficiency of the most established software tools performing exact pairwise sequence alignment on various computational architectures: CPU, GPU and Intel Xeon Phi.
Fig. 2 Alignment of various DyP-type peroxidase sequences from P. sapidus (PsaDyP), P. ostreatus (PosDyP, NCBI: CAK55151), B. adusta (BadDyP, NCBI: BAA77283), A. auricula-judae (AauDyP, NCBI: AFJ79723) and M. scorodonius (MsP1, NCBI: BOBK71).
These distributions were quantified with atomic force microscopy measurements, and a model was developed relating these length distributions to the change in nanotube alignment at various electric field strengths.
We prepared mRNA from the spleen of individuals of each species and performed RT-PCR experiments using two oligonucleotides designed on the alignment of various elasmobranch Igμ heavy chain sequences available in GenBank.
Meanwhile, pre-aligned sequences in PHYLIP format can be accepted by PALM as input to fulfill user requests with respect to alignment from various perspectives.
Finally, an amino acid sequence alignment between various RecA family proteins revealed that the equivalent amino acids to Arg72 in other aracheal RadA proteins or in eukaryotic Rad51 and Dmc1 were glycines, including Gly143 of yeast Rad51.
