Test on-line:

The programs usage in Scientific publications PROT_MAP
MaliN
MaliP
EST_map
SCAN2
Genome Comparison Browser

PROT_MAP

PLoS ONE
(2013), 8(1): e53525. doi:10.1371/journal.pone.0053525

A Genome-Wide Association Study Identifies Genomic Regions for Virulence in the Non-Model Organism Heterobasidion annosum s.s.

Dalman et al.,
Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden

...he gene annotations found in TC32-1 were transferred to the reference sequence using PROT_MAP, FGENESH-2 (SoftBerry, Mount Kisco, NY) and Artemis ...


PLoS ONE
(2011) 6(8): e22046. doi:10.1371/journal.pone.0022046

Spliceosomal Intron Insertions in Genome Compacted Ray-Finned Fishes as Evident from Phylogeny of MC Receptors, Also Supported by a Few Other GPCRs.

Zhang et al.,
Department of Biology, University of Padua, Padova, Italy, Abteilung fur Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universitat zu Kiel, Kiel, Germany

...To ensure correct gene structures of all putative GPCR genes, we predicted gene structures using GENSCAN [97], [98] and predictions were repeated using GENOMESCAN [97], [98], GENEWISE [99] and FGENESH/FGENESH+ [31]. Intron-exon structures were determined with the aid of GENEWISE [99] and/or PROT_MAP module of the Softberry software suite (website: www.softberry.org). ...


J Gen Virol
July 2011 vol. 92 no. 7 1500-1507 doi: 10.1099/vir.0.027706-0

Genotypic characterization of two bacterial artificial chromosome clones derived from a single DNA source of the very virulent gallid herpesvirus-2 strain C12/130

Stephen J. Spatz 1, Lorraine P. Smith 2, Susan J. Baigent 2, Lawrence Petherbridge 2 and Venugopal Nair 2
1Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, GA 30605, USA 2Institute for Animal Health, Compton, Berkshire RG20 7NN, UK

... 1988; Peng et al. 1995; Peng & Shirazi 1996a, b) were compared to pC12/130-10 and pC12/130-15 genomes using PROT_Map (SoftBerry, Mount Kisco, NY). Transcription factor-binding sites were investigated by using the TFsearch program (Maray et al. 1988; Peng ...


Virus Genes
2008 37:69–80 DOI 10.1007/s11262-008-0242-0

Clustering of mutations within the inverted repeat regions of a serially passaged attenuated gallid herpesvirus type 2 strain

Stephen J. Spatz, Cary Rue, Daniel Schumacher, Nikolaus Osterrieder
Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, 934 College Station Rd., Athens, GA 30605, USA Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA Institut fu.r Virologie, Philippstra.e 13, 10115 Berlin, Germany

... Published mRNA [20] and cDNA [28–30] data were compared to the 584Ap80 genome using PROT_MAP (SoftBerry, Mount Kisco, NY). ...


Virus Genes
Volume 35, Number 3 / December 2007 p. 753-766

Comparative sequence analysis of a highly oncogenic but horizontal spread-defective clone of Marek’s disease virus

Stephen J. Spatz et al.,
Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, 934 College Station Rd., Athens, GA 30605, USA

... PairwiseFLAG. Published mRNA and cDNA data were compared to the pRB-1B-5 genome using PROT_MAP (SoftBerry, Mount Kisco, NY). Multiple ...


Virus Genes
Volume 35, Number 1 / August 2007 p. 41-53

Polymorphisms in the repeat long regions of oncogenic and attenuated pathotypes of Marek’s disease virus 1

Stephen J. Spatz and Robert F. Silva
US Department of Agriculture, Southeast Poultry Research Laboratory, Agricultural Research Service, 934 College Station Rd, Athens, GA 30605, USA , US Department of Agriculture, Avian Disease and Oncology Laboratory, Agricultural Research Service, 3606 East Mount Hope Rd, East Lansing, MI 48823, USA

... Pub- lished mRNA and cDNA data were compared to the genomes of attenuated and nonattenuated strains of MDV using PROT_MAP (SoftBerry, Mount Kisco, NY). ...


Genetics
Vol. 176, 599-609, May 2007

The FLOWERING LOCUS T-Like Gene Family in Barley (Hordeum vulgare)

Sebastien Faure, Janet Higgins, Adrian Turner and David A. Laurie
John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom

... New gene predictions were made using FGENESH+ and PROT_MAP (http://sun1.softberry. com) for FT-like genes showing incorrect alignment within the PEBP domain and ...


J Gen Virol
88 (2007), 1080-1096

Comparative full-length sequence analysis of oncogenic and vaccine (Rispens) strains of Marek's disease virus

Stephen J. Spatz1, Lawrence Petherbridge2, Yuguang Zhao2 and Venugopal Nair2
1 Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, GA 30605, USA
2 Institute for Animal Health, Compton, Berkshire RG20 7NN, UK

... BMEC/ITRI). Published mRNA and cDNA data were compared with the CVI988 genome by using PROT_MAP (SoftBerry). Multiple protein ...


MaliN

Journal of Experimental Botany
2007 58(3):439-451;

Factors involved in root formation in Medicago truncatula

Nijat Imin*, Mahira Nizamidin, Tina Wu and Barry G. Rolfe
Australian Research Council Centre of Excellence for Integrative Legume Research, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, Canberra City, ACT 2601, Australia

... Then the PLETHORA genes were aligned using the program MaliN (Softberry Inc., NY, USA) and the forward degenerative primer, PLTconsF (CAACAYGGRAGRTGGCAAGCAAG ...


MaliP

MPMI
Vol. 24, No. 9, 2011, pp. 1051–1060. doi:10.1094/ MPMI -12-10-0281

A Dual-Targeted Soybean Protein Is Involved in Bradyrhizobium japonicum Infection of Soybean Root Hair and Cortical Cells

Libault et al.,
1 Division of Plant Sciences, National Center for Soybean Biotechnology, C.S. Bond Life Sciences Center, University of Missouri, Columbia 65211 U.S.A.; 2 Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis 63132 U.S.A.;

...Given the lack of functional annotation for GmNMNa, we used MaliP software to identify conserved domains. T...


EST_map

PLoS genetics
(2013). 9(1), e1003233. DOI:10.1371/journal.pgen.1003233

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

Condon et al.,
Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America

... The gene-prediction methods were: EST-based predictions with EST map (http://softberry.com) using raw ESTs and assembled EST contigs for each genome; homology-based predictions with Fgenesh+ [103] and Genewise ....


International Journal of Food Microbiology
Volume 157, Issue 2, 2 July 2012, Pages 202–209 DOI: 10.1016/j.ijfoodmicro.2012.05.008,

The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties

Jure Piskur et al.,
a Wine Research Centre, University of Nova Gorica, Slovenia b Department of Biology, Lund University, Sweden

... 2) homology-based — FGENESH+; Genewise (Birney and Durbin, 2000) seeded by BLASTx alignments against GenBank's database of non-redundant proteins (NR: http://www.ncbi.nlm. nih.gov/BLAST/), and 3) EST-based — EST_map (http://www.softberry.com/) seeded by ...


Fungal Genetics and Biology
Volume 49, Issue 3, March 2012, Pages 217–226 DOI: 10.1016/j.fgb.2012.01.007

The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction

Mahajabeen Padamsee et al.,
a Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, United States b Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, United States

... 2) homology-based – FGENESH +; Genewise (Birney and Durbin, 2000) seeded by BLASTx alignments against GenBank's database of non-redundant proteins (NR: http://www.ncbi.nlm. nih.gov/BLAST/), and (3) EST-based – EST_map (http://www.softberry.com/) seeded by ...


New Phytologist
Volume 194, Issue 4, pages 1001–1013, June 2012 DOI: 10.1111/j.1469-8137.2012.04128.x

Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen

Olson et al.,
1 Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ullsvag 26, 750 05 Uppsala, Sweden 2 US DOE Joint Genome Institute, Walnut Creek, CA 94598, USA

... based – FGENESH+, Genewise (Birney & Durbin, 2000) seeded by BLASTx (Altschul et al., 1990) alignments against GenBank's database of nonredundant proteins (NR: http://www.ncbi.nlm.nih. gov/BLAST/); and EST-based – EST_map (http://www.softberry.com/) seeded by ...


PLoS Pathog
8(12): e1003037. doi:10.1371/journal.ppat.1003037

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

Ohm et al.,
United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America

... The gene-prediction methods were: EST-based predictions with EST map (http://softberry.com) using raw ESTs and assembled EST contigs for each genome; homology-based predictions with Fgenesh+ [87] and Genewise...


Nature Biotechnology
29, 922–927 (2011) doi:10.1038/nbt.1976

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris.

Berka et al.,
Novozymes, Inc., Davis, California, USA. US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.

... was performed using ab initio Fgenesh 32 and Genemark-ES 33 ; homology-based Fgenesh+ 32 and Genewise 34 seeded by BLASTx alignments of NCBI's nr (nonredundant) protein database against the assembly; cDNA-based EST_map (http://www.softberry.com/) seeded ...


SCAN2

Annals of Translational Medicine
Vol 1, No 3 (October 2013) DOI:10.3978/j.issn.2305-5839.2012.12.01

The physiological roles of secretin and its receptor

Afroze et al.,
1Department of Medicine, Division Gastroenterology, 2Research, Central Texas Veterans Health Care System, 3Scott & White Digestive Disease Research Center, Scott & White, and Texas A&M Health Science Center, College of Medicine, Temple, TX 76504, USA;

... gene. Homology was analyzed using SCAN2 software from Softberry, http://linux1. softberry.com/berry.phtml?topic=scan2&group=programs&subgroup=scanh subsequently, % homology was calculated independently. Secretin ...


Folia Biologica
Volume 61, Numbers 3-4, August 2013 , pp. 149-153(5) DOI:10.3409/fb61_3-4.149

The Use of Primed in situ Synthesis (PRINS) to Analyze Nucleolar Organizer Regions (NORs) and Telomeric DNA Sequences in the Domestic Chicken Genome

Bugno-Poniewierska et al.,

... Comparative alignment analysis performed by SCAN2 software by Softberry (http://linux1.soft- berry.com/berry.phtml) for aligning two multi- megabyte-size nucleotide sequences revealed that our set of primers is partially complementary to 18S and 28S rDNA sequences (SHAO ...


Virus Genes
April 2012, Volume 44, Issue 2, pp 273-285 DOI: 10.1007/s11262-011-0696-3

Comparative full genome analysis of four infectious laryngotracheitis virus (Gallid herpesvirus-1) virulent isolates from the United States

S. J. Spatz et al.,
1. United States Department of Agriculture, Southeast Poultry Research Laboratory, Agricultural Research Service, Athens, GA, 30605, USA 2. BASE2BIO, Madison, WI, 53714, USA

... Homology searches were con- ducted using the NCBI program blastP with default settings. Multiple alignments of proteins and nucleotide sequences were generated using MAFFT [28], Multalin [3] and SCAN2 (Softberry.com). Results and discussion ...

Virus Genes
Volume 42, Issue 3 , pp 331-338 DOI: 10.1007/s11262-011-0573-0

Comparative genomic sequence analysis of the Marek’s disease vaccine strain SB-1

Stephen J. Spatz, Karel A. Schat
1. Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, GA, 30605, USA 2. Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA

... Homology searches were con- ducted using the NCBI program blastP with default set- tings. Multiple alignments of proteins and nucleotide sequences were generated using MAFFT [12] and SCAN2 (Softberry.com). Results and discussion Phylogenetic relatedness ...



African Journal of Biotechnology
Vol. 2 (12), pp. 714-718, December 2003
Available online at http://www.academicjournals.org/AJB

Minireview
Web-based bioinformatic resources for protein and nucleic acids sequence alignment

Kamel A. Abd-Elsalam
Molecular Markers Lab., Plant Pathology Research Institute, Agricultural Research Center, Orman 12619, Giza, Egypt.

... 16-SCAN2:: program for aligning two multimegabyte-size sequences. http://www.softberry.com/berry.phtml?topic=scanh&prg= SCAN2. derived ...


Nucleic Acids Research,
2003, Vol. 31, No. 13 3540-3545

PromH: promoters identification using orthologous genomic sequences

V. V. Solovyev* and I. A. Shahmuradov
Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY 10549, USA 1 Institute of Botany, Azerbaijan National Academy of Sciences, 370073 Baku, Azerbaijan
*To whom correspondence should be addressed. Tel: +1 914 242 3592; Fax: +1 914 242 3593; Email: victor@softberry.com Present address: I. A. Shahmuradov, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK

... The full-length sequences of gene pairs have been aligned by the SCAN2 program (http://softberry.com/berry.phtml?topic=scanh&prg=SCAN2), which can align ...


Genome Comparison Browser

The Plant Journal ,
2008 Volume 53 Issue 1, Pages 124 - 132

Low X/Y divergence in four pairs of papaya sex-linked genes

Qingyi Yu et al.,
Hawaii Agriculture Research Center, Aiea, HI 96701, USA

... The predicted transcripts were tested by RT-PCR, and the BAC sequences were aligned using a genome comparison browser (http://sun1.softberry.com). ...


Molecular Genetics and Genomics ,
Volume 278, Number 2 / August 2007 p. 177-185

Chromosomal location and gene paucity of the male specific region on papaya Y chromosome

Qingyi Yu et al.,
Hawaii Agriculture Research Center, Aiea, HI 96701, USA

... The predicted transcripts were tested by RT-PCR. Genome comparison browser (http://www.sun1.softberry.com) was used for comparative sequence analysis. RT-PCR ...



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