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Simply put, OligoLocator will identify the position of oligonucleotides (primers and probes) based on comparisons with a reference sequence. The following oligonucleotides are supported:
Several reports have demonstrated the role of miRNAs, small noncoding RNA molecules of ∼22 nucleotides in length that function as inhibitors of post-transcriptional gene silencing, in the regulation of tumor development and progression. Aberrant miRNA expression profiles have been demonstrated in malignancies of breast, lung, colon, cervical, and oral squamous cell carcinoma. Recently, two studies have shown that miRNA play a critical role in the regulation of the innate immune response to bacteria and viral infections and that pathogen-derived miRNAs play a decisive role in the immune response. These findings have opened new perspectives for the treatment of cancer and autoimmune diseases by targeting miRNA.
Oligonucleotides Targeting miRNAs:
Oligonucleotides that target miRNAs may interfere with the proper functioning of miRNAs. For example, the exact in vivo function of miR-146a is not known. Thus, antisense oligonucleotides to miR-146a may interfere with the proper functioning of miR-146a, which may have an impact on cell proliferation and neoplasia. Similarly, miR-223 has been demonstrated to play an important role in the regulation of monocyte/macrophage phagocytosis, and inhibition of miR-223 may have anti-inflammatory effects. Thus, an oligonucleotide designed to target miR-223 may play a role in the regulation of cell proliferation, apoptosis, and inflammation in normal and tumor cells. Because of the importance of miRNAs and their potential therapeutic application, it is important to be able to predict their exact position within an mRNA sequence.
Antisense technology is emerging as an effective means for a variety of diagnostic, therapeutic, and research applications. The small size and the ease with which the antisense oligonucleotides are synthesized make them a highly desirable compound for use as therapeutic agents. For an antisense oligonucleotide to be useful as a therapeutic agent, it is desirable that it be stable in vivo, have a high biological activity, and be able to penetrate the cell membrane. Oligonucleotides have been developed that are capable of binding to target mRNA, thereby blocking translation of the
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OligoLocator is an open source Java based software tool designed to identify the position of oligonucleotides within nucleic acid sequences in which they may be involved in any polymorphic variations.
OligoLocator uses the MD5 algorithm to find subsequences which are almost identical to an oligonucleotide of interest. The algorithm uses three different oligonucleotides (called “DETONATE”, “MEET”, and “MITER”) which are smaller versions of the original oligonucleotide. These oligonucleotides are created by removing each of the n-1, n-2 and n-3 base pairs of the original oligonucleotide.
“DETONATE” – the oligonucleotide is deleted from the front so that the oligonucleotide length is n-3, n-2 and n-1.
“MEET” – the oligonucleotide is deleted from the end so that the oligonucleotide length is n-3, n-2 and n-1.
“MITER” – the oligonucleotide is deleted from both the front and end, so the oligonucleotide length is n-3, n-2, n-1 and the inner deletion so that only n-1, n-2 and n-3 are deleted from the inner region.
MD5 does not require the input to be in the exact same sequence as the oligonucleotides. The program performs a basic MD5 hashing on the oligonucleotides and then outputs the position of the match within a larger sequence using binary search.
“OligoLocator” can be used to find the position of a single oligonucleotide within a larger sequence. To identify multiple oligonucleotides the program can be set to find multiple oligonucleotides within a single sequence file. Once the oligonucleotide has been identified OligoLocator can also find the position of a multiple oligonucleotides within a larger sequence.
“OligoLocator” does not report mismatches as “false positives”. Where possible OligoLocator sets multiple mismatches as the last base in the oligonucleotide.
“OligoLocator” uses the -f option to perform a forward search and the -b option to perform a backward search. The -f flag is specified
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OligoLocator is a Java based application designed to identify the position of oligonucleotides within nucleic acid sequences with varying degrees of mismatch between the two. OligoLocator is provided as free software under the GNU General Public License.
Version 18.104.22.168 of the OligoLocator application was released on 02/15/2010. OligoLocator features the following features:
• The OligoLocator uses a simple, visual approach to assist the user in identifying oligonucleotide positions within a nucleic acid sequence.
• The OligoLocator provides a simple method to determine the position of oligonucleotides within a nucleic acid sequence, including DNA or RNA.
• The OligoLocator provides a standard format output file that can be opened in other software packages.
• Multiple oligonucleotides can be specified using regular expressions.
• The user can specify a set of oligonucleotides using a template.
• The location of each oligonucleotide may be specified using one of four possible approaches:
1) Direct Count: The position is the actual base count from the start of the nucleic acid sequence (1).
2) Relative Count: The position is the relative position within the sequence where the desired oligonucleotide is found (e.g., the position of the third oligonucleotide in the sequence above).
3) Direct Slice: The position is the initial base count of the desired oligonucleotide within the sequence.
4) Relative Slice: The position is the relative position of the oligonucleotide within the sequence (e.g., starting with the third base of the first oligonucleotide in the sequence above).
Select Oligonucleotides using a template:
Some oligonucleotides may be difficult to identify accurately within a nucleic acid sequence. To facilitate the identification of these oligonucleotides OligoLocator provides an easier way to identify the specific oligonucleotides within a nucleic acid sequence. To assist in the identification of oligonucleotides OligoLocator provides a generic template that contains a list of oligonucleotides. The user may specify which oligonucleotides on the template should be selected. The user can select an oligonucleotide from a list of oligonucleotides with the sequence
What’s New In OligoLocator?
– Provides a graphical interface for the user to choose a nucleic acid sequence and enter the position of the oligonucleotide(s) of interest.
– Does not require prior knowledge of primer sequences and oligonucleotide lengths.
– Computes the position of oligonucleotides in relation to the sense or antisense strand.
– The program provides a link to NCBI for the sequences.
– The program can also return a link to the NCBI BLAST website where the particular oligonucleotide sequence can be viewed directly, with the corresponding sequence for the locator.
– Users can upload sequences for analysis.
– The information on the position of the oligonucleotides and the links to NCBI can be saved so that the user can compare the position of oligonucleotides for any given sequence at a later time.
– A link to the tutorial page is also provided.
The current version of OligoLocator is version 2.0.
The version history is as follows:
Version 2.0 was released March 6, 2009.
The BLAST toolkit ( is an open-source project that helps researchers explore similarities between sequences and compare regions of interest and sequences with the BLAST algorithm, a set of tools for high-speed, nucleotide sequence-based searches. For reviews, see (Woese (1990) Proc. Natl. Acad. Sci. USA, 87:4576-4579; Altschul et al., (1990) J. Mol. Biol., 215:403-410; Madden and Olovnikov (2004) in Protein Science, 13:4:862-869.) The BLAST algorithm performs local alignments and identifies genes and proteins in the BLAST output in the form of position-specific scoring matrices (PSSMs), which can then be compared with those of other proteins.
The OligoLocator software uses the BLAST algorithm to identify DNA or RNA oligonucleotides (bases 2-30) and the sequences flanking them.
The software is designed to be simple to use and requires very little prior knowledge of the principles of BLAST. This software is designed for the non-expert and should work well with shorter sequences (up to 1500 bp). For longer sequences a separate program, NotBlast, is available.
1) Windows XP/Vista/7/8
2) 2.4 GHz Pentium 4 or AMD Dual Core processor
3) 2 GB RAM or more
4) 12 MB DirectX 9 or later or OpenGL 1.3 compatible graphics card
5) Windows Media Player (wmp10) or Windows Media Center (wmc10)
6) DirectX SDK (optional)
7) WAV files
8) NFS install disk
9) 60 MB free hard disk space
Q1: Which version of