FISH 0.2 – Fast Genotype Imputation with Segmental Hidden Markov model.

FISH 0.2

:: DESCRIPTION

FISH is a java program for fast and accurate diploid genotype imputation.

::DEVELOPER

Dr. Lei Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 FISH

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 31. [Epub ahead of print]
FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model.
Zhang L1, Pei YF, Fu X, Lin Y, Wang YP, Deng HW.

FisHiCal 1.1 – Iterative FISH-based Calibration of Hi-C Data

FisHiCal 1.1

:: DESCRIPTION

FisHiCal integrates Hi-C and FISH data, offering a modular and easy-to-use tool for chromosomal spatial analysis.

::DEVELOPER

Yoli Shavit, Fiona Kathryn Hamey and Pietro Lio’

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • R

:: DOWNLOAD

 FisHiCal

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 23. pii: btu491.
FisHiCal: an R package for iterative FISH-based calibration of Hi-C data.
Shavit Y, Hamey FK, Lio P.

PROBER 2.1 – Fish Oligo Probe Design Software

PROBER 2.1

:: DESCRIPTION

PROBER is an oligonucleotide primer design software application that can generate highly specific probes for use in fluorescence in-situ hybridization (FISH) and other in-situ labeling methods by densely tiling relatively small genomic intervals.  Generating Tiling Oligonucleotide Probes (TOPs) requires software capable of masking repetitive genomic sequences and saturating unique contiguous blocks with small (100-2000bp), DNA probes that will generate a single, strong fluorescent signal for regions as small as a single gene.

::DEVELOPER

Nicholas Navin

:: SCREENSHOTS

PROBER

:: REQUIREMENTS

  • Windows
  • .net framework

:: DOWNLOAD

 PROBER

:: MORE INFORMATION

Citation

Navin N, Grubor V, Hicks J, Leibu E, Thomas E, Troge J, Riggs M, Lundin P, Maner S, Sebat J, Zetterberg A, Wigler M.
PROBER : oligonucleotide FISH probe design software.
Bioinformatics. 2006 Jun 1. Epub PMID: 16740623

FISH – Fast Indexing for Spaced-seed Hashing

FISH

:: DESCRIPTION

FISH is a novel algorithm,which based on the indexing of small blocks that can be combined to obtain the hashing of spaced-seeds of any length. The method exploits the fast computation of the hashing of runs of consecutive 1 in the spaced seeds, that basically correspond to k-mer of the length of the run.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

FISH

:: MORE INFORMATION

Citation

BMC Bioinformatics, 19 (Suppl 15), 441 2018 Nov 30
Efficient Computation of Spaced Seed Hashing With Block Indexing
Samuele Girotto , Matteo Comin , Cinzia Pizzi

MitoAnnotator – Annotating Fish Mitogenomic Sequence

MitoAnnotator

:: DESCRIPTION

MitoFish is a comprehensive and standardized fish mitochondrial genome database.

MitoAnnotator is a pipeline for annotating fish mitogenomic sequence fully automatically and accurately just in five minutes.

::DEVELOPER

Atmosphere and Ocean Research Institute, the University of Tokyo,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Biol Evol. 2013 Nov;30(11):2531-40. doi: 10.1093/molbev/mst141. Epub 2013 Aug 16.
MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline.
Iwasaki W1, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M, Nishida M.

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