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OligoWiz
A powerful tool for microarray probe design that allows for integration of sequence annotation, such as exon/intron structure, untranslated regions (UTRs), transcription start site, etc. In addition to probe selection according to a series of probe quality parameters, cross-hybridization, T(m), position in transcript, probe folding and low-complexity, the program facilitates automatic placement of probes relative to the sequence annotation. The program also supports automatic placement of multiple probes per transcript. Together these facilities make advanced probe design feasible for scientists inexperienced in computerized information management.
OligoArray
Designs specific oligonucleotides at the genomic scale. OligoArray computes gene-specific and secondary structure-free oligonucleotides for genome-scale oligonucleotide microarray construction. This program also uses the Lempel-Ziv (LZ) sequence complexity criteria, and allows the design of oligonucleotides for use on microarrays for gene expression profiling. It can manage neither polymorphism nor splicing variants, except by considering each variant as a different input sequence.
AffyProbeMiner
Allows computation or retrieval of redefined Affymetrix probe sets. AffyProbeMiner uses mRNA RefSeqs and validated complete coding sequences in GenBank to (1) regroup the individual probes into consistent probe sets and (2) remap the probe sets to the correct sets of mRNA transcripts. It was used to study several biologically and biomedically important research problems, including enhanced characterization of the NCI-60 cancer cell line. The command-line code allows the user to generate the altered mapping files.
ProDesign
A tool developed for the selection of oligonucleotide probes to detect members of gene families present in environmental samples. Gene family-specific probe sequences are generated based on specific and shared words, which are found with the spaced seed hashing algorithm. To detect more sequences, those sharing some common words are re-clustered into new families, then probes specific for the new families are generated. ProDesign is very flexible in that it can be used for designing probes for detecting many genes families simultaneously and specifically in one or more genomes. Neither the length nor the melting temperature of the probes needs to be predefined. The program provides biologists with a powerful tool for an easy, rapid and flexible design of oligonucleotide probes for environmental microarrays and related applications.
OligoSpawn
Investigates and selects oligos from unigenes sequences. OligoSpawn is composed of three main panels: (i) popular oligo design, that allows users to pick oligo from sequences; (ii) popular oligo check, that depicts correspondence between popular oligos and sequences; and (iii) unique oligo design, that detects oligos that are unique into sequences. The web application can perform only files of 50 megabases and less. To perform larger files, users have to install the desktop version of the software.
PROBEmer
Obsolete
A web-based software tool that enables a researcher to select optimal oligos for PCR applications and multiplex detection platforms including oligonucleotide microarrays and bead-based arrays. Given two groups of nucleic-acid sequences, a target group and a non-target group, the software identifies oligo sequences that occur in members of the target group, but not in the non-target group. To help predict potential cross hybridization, PROBEmer computes all near neighbors in the non-target group and displays their alignments. Because it does not rely upon multi-alignments, it can be applied to sequences which are not similar (e.g. genes in a single organism) or to variations of a gene in many organisms (e.g. 16S rRNA gene).
Pigeons / Photographically InteGrated En-suite for the OligoNucleotide Screening
Obsolete
Allows users to input and analyse microarray data from the Xspecies microarray approach. Pigeons employs quantile normalization to address the comparability of intensity distributions between arrays. It is focused around visualization and interactive studies of the datasets at the probe level. It also provides a specific visualization interface to facilitate navigation through the hundreds of thousands of Affymetrix oligonucleotides.
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HuGChip / Human Gut Chip
Assists users in evaluating human gut microbiota. HuGChip is a phylogenic microarray, generated thanks to the PhylArray software, which encompasses 8x15k probes with three probe replicates. The database includes explorative probes with the aim of permitting the detection of unknown bacteria without strong taxonomic evidences. Moreover, it authorizes the analysis of over 16 different samples per run, in order to decrease costs as well as limiting inter microarray bias.
PhylOPDb
An online resource for a comprehensive phylogenetic oligonucleotide probe database. PhylOPDb provides a convivial and easy-to-use web interface to browse both regular and explorative 16S rRNA-targeted probes. Such probes set or subset could be used to globally monitor known and unknown prokaryotic communities through various techniques including DNA microarrays, polymerase chain reaction (PCR), fluorescent in situ hybridization (FISH), targeted gene capture or in silico rapid sequence identification.
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