Tag: cDNA

ANGLE – Predict Coding Sequences in low quality cDNA

ANGLE

:: DESCRIPTION

ANGLE (Anti Noise Gene Locator Engine) is a new program for predicting coding sequences in low quality cDNA. To achieve error-tolerant prediction, ANGLE uses a machine-learning approach, which makes better expression of coding sequence maximizing the use of limited information from input sequences.

::DEVELOPER

Kana Shimizu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ANGLE

:: MORE INFORMATION

Citation

Shimizu, K., Adachi, J., and Muraoka, Y. (2006)
ANGLE: a sequencing errors resistant program for predicting protein coding regions in unfinished cDNA.
J Bioinform Comput Biol 4, 649-664

Splign 20150223 – Compute cDNA-to-Genomic / Spliced Sequence Alignment

Splign 20150223

:: DESCRIPTION

Splign is a utility for computing cDNA-to-Genomic, or spliced sequence alignments. At the heart of the program is a compartmentization algorithm which identifies possible gene duplications, and a refined alignment algorithm recognizing introns and splice signals.

Splign Online Version

::DEVELOPER

NCBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

Splign

:: MORE INFORMATION

Citation

Y.Kapustin, A.Souvorov, T.Tatusova and D.Lipman.
Splign: algorithms for computing spliced alignments with identification of paralogs.
Biology Direct, May 2008.

F-SCAN 1.3 – Fluorescently Probed cDNA Microarray Analysis

F-SCAN 1.3

:: DESCRIPTION

F-SCAN is a software of Fluorescently Probed cDNA Microarray Analysis

::DEVELOPER

Analytical Biostatistics Section,NIH

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

 F-SCAN

:: MORE INFORMATION

Citation:

A. J. Carlisle, V. V. Prabhu, A. Elkahloun, J. Hudson, J. M. Trent, W. M. Linehan, E. D. Williams, M. R. Emmert-Buck, L. A. Liotta, P. J. Munson, and D. B. Krizman;
“Development of a Prostate cDNA Microarray and Statistical Gene Expression Analysis Package“;
Molecular Carcinogenesis 28:12-22 (2000)

SignalViewer – Image Analysis of cDNA Microarrays

SignalViewer

:: DESCRIPTION

SignalViewer is a Software Application for Image Analysis of cDNA Microarrays

::DEVELOPER

Fred Hutchinson Cancer Research Center

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 SignalViewer

:: MORE INFORMATION

Citation

Laws RJ, Bergemann TL, Quiaoit F, Zhao LP.
SignalViewer: analyzing microarray images.
Bioinformatics. 2003 Sep 1;19(13):1716-7.

Pairagon 1.1 – Pair-HMM based cDNA-to-genome Alignment

Pairagon 1.1

:: DESCRIPTION

Pairagon is a pair-HMM based cDNA-to-genome alignment program.

::DEVELOPER

The Brent Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Pairagon

:: MORE INFORMATION

Citation

Lu D.V., Brown R.H., Arumugam M., Brent M.R.. 2009.
“Pairagon: A Highly Accurate, HMM-based cDNA-to-genome Aligner.”
Bioinformatics 25 (13): 1587-1593.

seqjoin – Predict Complete cDNA Insert Sequence

seqjoin

:: DESCRIPTION

seqjoin is used to predict the complete cDNA insert sequence of partially sequenced cDNA clones. The clones’ partial experimental sequence are matched to a database of complete cDNA sequence. If a match is found, the clone’s insert sequence is predicted from the vector sequence, the sequence of the database cDNA sequence entry that was matched and the experimental, partial clone sequence. seqjoin is based on the output of the sequence analysis programs phred, phrap, cross_match and also uses the Emboss package.

::DEVELOPER

Protein Structure Factory

:: REQUIREMENTS

:: DOWNLOAD

seqjoin

:: MORE INFORMATION

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