GeSeq - 3rd Party Software

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ARAGORN

Laslett D and Canback B (2004) ARAGORN, a program for the detection of transfer RNA and transfer-messenger RNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16

 

ARWEN

Laslett D and Canback B (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 24: 172-175

 

BLAT

Kent WJ (2002) BLAT - The BLAST-like alignment tool. Genome Research 12: 656-664

 

Chloë

Developed by the lab of Ian Small (unpublishd)

 

Infernal

Nawrocki EP and Eddy SR (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29: 2933-2935

 

nhmmer

Wheeler TJ and Eddy SR (2013) nhmmer: DNA homology search with profile HMMs. Bioinformatics 29: 2487-2489

 

MFannot

Developed by the labs of B. Franz Lang and Gertraud Burger (unpublished)

 

MUSCLE

Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797

 

Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113

 

OGDRAW

Greiner S, Lehwark P and Bock R (2019) OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research 47: W59-W64

 

Lohse M, Drechsel O, Kahlau S and Bock R (2013) OrganellarGenomeDRAW - a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Research 41: W575-W581

 

Lohse M, Drechsel O and Bock R (2007) OrganellarGenomeDRAW (OGDRAW) - a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Current Genetics 52: 267-274

 

TranslatorX

Abascal F, Zardoya R and Telford MJ (2010) TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Research 38: W7-W13

 

tRNAscan-SE v2.0.7

Chan PP, Lin BY, Mak AJ and Lowe TM (2019) tRNAscan-SE 2.0: Improved detection and functional classification of transfer RNA genes. bioRxiv 614032

 

tRNAscan-SE v1.3.1

Lowe TM and Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25: 955-964