Jaya Prakash Dr. Elgin, Dr. Shaffer Biology 434W 10 February 2017 Finishing of DEUG4927010 Abstract The goal of this project was to prepare the DEUG4927010 contig—which covers the terminal 99,279 bases from the fourth chromosome of Drosophila eugracilis—for annotation. In the initial assembly of this project, there were 122 high quality discrepancies and 49 regions with low depth of coverage. N...

The farthest string problem (FARTHEST STRING) is one of the core problems in the field of consensus word analysis and several biological problems such as discovering potential drugs, universal primers, or unbiased consensus sequences. Given k strings of the same length L and a nonnegative integer d, FARTHEST STRING is to find a string s such that none of the given strings has a Hamming distance...

We present a computational scheme to search for the most common motif, composed of a combination of sequence and structure constraints, among a collection of RNA sequences. The method uses a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments from pairwise comparisons. The overa...

Supplemental Figure 1. Alignments of newly characterized DeuSINE families and subfamilies. (A) AmnSINE1 from human, (B) AmnSINE1 from chicken, (C) LmeSINE1a from coelacanth, (D) LmeSINE1b from coelacanth, (E) SINE3_IP from catfish, (F) OS-SINE1 from rainbow trout, (G) SacSINE1 from dogfish shark, (H) EbuSINE1 from hagfish, (I) EbuSINE2 from hagfish, and (J) BflSINE1 from amphioxus. The top sequ...

Primaclade is a web-based application that accepts a multiple species nucleotide alignment file as input and identifies a set of polymerase chain reaction (PCR) primers that will bind across the alignment. Primaclade iteratively runs the Primer3 application for each alignment sequence and collates the results. Primaclade creates an HTML results page that recaps the original alignment, provides ...

We have calculated the consensus sequence for human mitochondrial DNA using over 800 available sequences. Analysis of this consensus reveals an unexpected lack of diversity within human mtDNA worldwide. Not only is more than 83% of the mitochondrial genome invariant, but in over 99% of the variable positions, the majority allele was found in at least 90% of the individuals. In the remaining 0.2...

[Internal Report] Saliya Ekanayake School of Informatics and Computing, Indiana University [email protected] ABSTRACT Determination of biologically related clusters of sequences is important bioinformatics analyses. The similarity between sequences is generally assessed based on their alignments with one another. This could be used with a clustering algorithm to determine groups of sequen...

We introduce visualization and comparison of consensus sequences (VisCoSe) as a WWW service and a stand-alone command line Perl script for visualizing and comparing consensus sequences of protein and nucleotide sequences. VisCoSe is the only interface available that simultaneously calculates consensus sequences of multiple data sets and automatically compares these consensus sequences. Furtherm...