The document provides an overview of several agricultural databases and genome research programs. It discusses the National Center for Biotechnology Information (NCBI) and databases it maintains, including GenBank, PubMed, PubChem, dbSNP, and others. It also describes other plant-focused databases like Gramene, GrainGenes, PlantGDB, TIGR, UK CropNet, and databases for specific crops like MaizeDB, TAIR, Rice Genome Research Program, and the US Wheat Genome Project. Genome assembly and analysis software is also briefly mentioned.

1. SUBMITTED BY :-
NARAYAN DHAR AWASTHI
M. SC. (Ag), Department of Genetics & Plant Breeding, Chaudhary Charan Singh
University, Meerut
TOPIC - AGRICULTURAL DATABASES

2. Contents:-
 Introduction of NCBI databases
 GenBank
 TIGR
 UK CropNet
 PlantGDB
 GrainGenes
 Gramene
 Komugi
 Rice Genome Research Program
 Us Wheat Genome Project
 GMO food Resources
 MaizeDB
 TAIR
 Genome Search Software
 Phred/Phrap/Consed
 Cross-Match
 Staden package
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3. Introduction of NCBI
 NCBI stand for National Center for Biotechnology Information.
 The establishment of NCBI in November of 1988.
 The NCBI located in Bethesda, Maryland
 NCBI is part of the United States National Library of Medicine(NLM),a branch
of the National Institutes of Health (NIH).
 The NCBI houses a series of databases relevant to biotechnology and
biomedicine and is an important resource for bioinformatics tools and
services.
 Major databases include GenBank for DNA sequence and PubMed, a
bibliographic literature.
 All these databases are available online through the Entrez search engine.
………….
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5. Popular resources of NCBI
 PubMed
 Bookshelf
 PubMed Central
 PubMed Health
 BLAST
 Nucleotide
 Genome
 SNP
 Gene
 Protein
 PubChem
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6. PubMed
 PubMed comprises more than 28 million citations for biomedical literature
from MEDLINE, life science journals, and online books.
 Citations may include links to full-text content from PubMed Central and
publisher web sites.
 1996—PubMed—NCBI introduces PubMed, a freely accessible bibliographic
retrieval system to the entire MEDLINE database.
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Contact
Research center United States National Library of
Medicine (NLM)
Release date January 1996; 22 years ago
Access
Website www.ncbi.nlm.nih.gov/pubmed/

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8. Bookshelf
 Bookshelf provides free online access to books and documents in life science
and healthcare.
 Search, read, and discover.
 2001—Bookshelf—The new Entrez database is introduced to provide free
access to books and documents in the life sciences and healthcare fields.
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10. PubMed Central
 PubMed Central (PMC) is a free full-text archive of biomedical
and life sciences journal literature at the U.S. National
Institutes of Health's National Library of Medicine (NIH/NLM).
 2000—PubMed Central—NCBI debuts its free
full-text digital archive of biomedical and life sciences
journal literature.
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PubMed Central
Producer United States
National Library of
Medicine (United
States)
Access
Cost Free
Coverage
Disciplines Medicine
Record depth Index, abstract &
full-text
Format coverage Journal articles
Links
•Website
•Title list

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12. BLAST
 BLAST stand for Basic Local Alignment Search Tool is an algorithm for
comparing primary biological sequence information, such as the amino-
acid sequences of proteins or the nucleotides of DNA sequences.
 1990—BLAST—the Basic Local Alignment Search Tool (BLAST) is introduced;
optimized for speed, the sequence comparison algorithm quickly finds similar
sequences to one’s query.
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BLAST
Developer(s) Altschul SF, Gish W, Miller W, Myers
EW, Lipman DJ, NCBI
Stable release 2.7.0+ / 10 October 2016; 18 months
ago
Operating system UNIX, Linux, Mac, MS-Windows
Type Bioinformatics tool
License Public domain

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14. PubChem
 PubChem is a database of chemical molecules and their activities against
biological assays.
 The system is maintained by the National Center for Biotechnology
Information (NCBI), a component of the National Library of Medicine, which is
part of the United States National Institutes of Health(NIH).
 PubChem can be accessed for free through a web user interface.
 Millions of compound structures and descriptive datasets can be freely
downloaded via FTP.
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Content
Description PubChem
Organisms Humans and
other animals
Contact
Research
center
NCBI
Primary
citation
PMID 1587918
0
Access
Website https://pubc
hem.ncbi.nl
m.nih.gov/
Download
URL
FTP
Miscellaneous
License Public
domain

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16. dbSNP
 Database of single nucleotide polymorphisms (SNPs) and multiple small-scale
variations that include insertions/deletions, microsatellites, and non-
polymorphic variants.
 Come from 1998.
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Data format ASN.1, Fasta, XM
L
Website www.ncbi.nlm.n
ih.gov/projects/
SNP/

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18. Protein databases
 The Protein database is a collection of sequences from several sources,
including translations from annotated coding regions in GenBank, RefSeq and
TPA, as well as records from SwissProt, PIR, PRF, and PDB.
 Protein sequences are the fundamental determinants of biological structure
and function
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20. Nucleotide databases
 The Nucleotide database is a collection of sequences from several sources,
including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript
sequence data provide the foundation for biomedical research and discovery.
 The three databases, DDBJ (Japan), GenBank (USA) and European Nucleotide
Archive (Europe), are repositories for nucleotide sequence data from all
organisms. ... These three databases are primary databases, as they house
original sequence data.
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21. GenBank
 The GenBank sequence database is an open access, annotated
collection of all publicly available nucleotide sequences and
their protein translations.
 GenBank set up in 1979 at the LANL (los Alamos).
 This database is produced and maintained by the National Center for
Biotechnology Information (NCBI) as part of the International Nucleotide
Sequence Database Collaboration (INSDC).
 The National Center for Biotechnology Information is a part of
the National Institutes of Health in the United States.
 1.dbEST.
 2.UNiGene.
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GenBank
Content
Description Nucleotide sequences for more than
300,000 organisms with supporting
bibliographic and biological annotat
Data types
captured
•Nucleotide sequence
•Protein sequence
Organisms All
Contact
Research center NCBI
Primary citation PMID 21071399
Release date 1982; 36 years ago
Access
Data format •XML
•ASN.1
•Genbank format
Website NCBI
Download URL ncbi ftp
Web service URL •eutils
•soap
Tools
Web BLAST
Standalone BLAST
Miscellaneous
License Unclear
[1]

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23. dbEST
 EST is Short subsequence of cDNA.
 dbEST is a division of GenBank established in 1992. As for GenBank, data in
dbEST is directly submitted by laboratories worldwide and is not curated.
 Expressed Sequence Tags (ESTs) are short (usually <1000 bp), single-pass
sequence reads from mRNA (cDNA).
 They represent a snapshot of genes expressed in a given tissue and/or at a
given developmental stage.
 They are tags (some coding, others not) of expression for a given cDNA
library.
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26. UniGene
 UniGene is an NCBI database of the transcriptome and thus, despite the
name, not primarily a database for genes.
 Each entry is a set of transcripts that appear to stem from the same
transcription locus (i.e. gene or expressed pseudogene).
 Transcriptome- the sum total of all the messenger RNA molecules
expressed from the genes of an organism.
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28. TIGR
 TIGR stand for Trst(Trieste) Istra(Istria) Gorica(Gorizia) Reka(Rijeka).
 The TIGR Plant Transcript Assemblies database is a repository of sequences
collected for the construction of transcript assemblies.
 The TIGR Gene Index databases (TGI) (http://www.tigr.org/tdb/tgi) are
constructed using all publicly available expressed sequence tags (EST) and
known gene sequence data stored in GenBank for each target species.
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30. U.K. CropNet
 The UK Crop Plant Bioinformatics Network (UK CropNet) was established in
1996 in order to harness the extensive work in genome mapping in crop
plants in the UK.
 Since this date we have published five databases from our central UK
CropNet WWW site (http://synteny.nott.ac.uk/ ) with a further three to
follow shortly.
 UK CropNet is a collaborative project with a membership of six groups, each
making a major contribution to plant genome analysis in the UK.
 Arabidopsis (University of Nottingham),
 Barley and Potato (Scottish Crop Research Institute),
 Brassicas (John Innes Centre),
 Cereals (John Innes Centre),
 Comparative Genome Analysis (John Innes Centre)
 Forage Grasses (Institute of Grassland and Environmental Research).
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32. PlantGDB
 PlantGDB ( http://www.plantgdb.org/ ) is a database of molecular sequence
data for all plant species with significant sequencing efforts.
 The database organizes EST sequences into contigs that represent tentative
unique genes. ... Genome sequence fragments are assembled similarly.
 The goal of the PlantGDB web site is to establish the basis for identifying sets
of genes common to all plants or specific to particular species by integrating a
number of bioinformatics tools that facilitate gene prediction and cross‐
species comparisons.
Con………….
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34. GrainGenes
 GrainGenes is an International database for Genetic and genomic information
about Triticeae species.(http://www.acedb.org)
 GrainGenes, a database for Triticeae and Avena, is a comprehensive resource
for molecular and phenotypic information for wheat, barley, rye, and other
related species, including oat.
 The GrainGenes database project was launched by the U.S. Department of
Agriculture in 1992.
 Current GrainGenes Team Members,
Lead Scientist Curator, System Administrator
TANER Z. SEN GERARD R.LAZO
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35. GSP(Genome Specific Primers)
 In a polyploid species, genes from the homoeologous genomes exhibit a very
high sequence similarity, especially in the coding regions.
 This makes it difficult to design genome-specific primers to amplify specific
sequences from the individual genomes in the polyploid genome background.
 Development of genome-specific primers for important genes in polyploid
species is very useful and critical not only for the study of sequence diversity
and association mapping of genes in natural populations, but also for the
development of gene-based functional markers for marker-assisted breeding.
 GSP is a powerful web-based platform for designing genome-specific primers
that can distinguish the sequences among different genomes in a polypoid
species
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36. PIECE-
 PIECE-Stand for Plant Intron Exon Comparison and Evolution database.
 PIECE is a plant gene structure comparison and evolution database with 25
species.
 Annotated genes were extracted from the species and classified based on
Pfam motif.
 Phylogenetic tree was reconstructed for each gene category integrated exon-
intron and protein motif information.
 Both the sequences and gene structure information for each identified gene
are freely available for online access on the PIECE website.
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38. CMap
 CMap is the official map display for the new GrainGenes
database, GrainGenes SQL. It also allows the maps to be compared side by
side much more satisfactorily.
 Currently GrainGenes CMap includes two Data Sources:
 GrainGenes
 Wheat Composite
 Data Source GrainGenes contains the same set of maps that can be viewed
with the ACEDB map display in GrainGenes Classic.
 The two databases are synchronized weekly.
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39. Gramene
 Gramene is a curated, open-source, integrated data resource for comparative
functional genomics in crops and model plant species.
 Tools
 HMMER is a free and commonly used software package for sequence analysis
written by Sean Eddy.
 Its general usage is to identify homologous protein or nucleotide sequences,
and to perform sequence alignments.
 It detects homology by comparing a profile-HMM to either a single sequence
or a database of sequences.
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HMMER Quickly search our genomes for your
protein sequence.
BLAST/BLAT Search our genomes for your DNA or
protein sequence.
50MB
Assembly
Converter
Map (liftover) your data's coordinates to
the current assembly.

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41. Komugi

KOMUGI is an integrated database of wheat created by Japanese researchers in
wheat sciences. "Komugi" is a Japanese word meaning wheat.
 This database was originally created in 1996 by a voluntary group of Japanese
scientists who were concerned about the genetic stocks of wheat (the
genus Triticum) and related species (the genus Aegilops) conserved in Japanese
institutions.
 The genetic stocks include the original accessions of Triticum and
Aegilops collected during expeditions led by the late Dr. H. Kihara and his
colleagues to their places of origin.
 Tools-
BLASTScope
Genomepoint
Ez-cutter
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43. Rice Genome Research Program
 The Rice Genome Research Program (RGP) is an integral part of the
Japanese Ministry of Agriculture, Forestry and Fisheries (MAFF) Genome
Research Project.
 It is jointly coordinated by the National Institute of Agrobiological Sciences
(NIAS), a government research institute under MAFF and the Society for
Techno-innovation of Agriculture, Forestry and Fisheries (STAFF), a semi-
private research organization managed and supported by MAFF and a
consortium of some twenty Japanese companies.
 The research is funded with yearly grants from MAFF and additional funds
from the Japan Racing Association (JRA).
 The program started in October 1991 and the first phase continued through
1997 resulting in the establishment of some of the basic tools of rice genome
analysis.
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44. A Complete sequence of rice chromosome-1
 The rice species Oryza sativa is considered to be a model plant because of its
small genome size, extensive genetic map, relative ease of transformation
and synteny with other cereal crops. Here we report the essentially complete
sequence of chromosome 1, the longest chromosome in the rice genome.
 Rice genome size-430mb,No. of gene present 32000-50000.
Received:04 April 2002
Accepted:19 September 2002
Published:21 November 2002.
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46. Links related to PGP

Rice Genome
Oryzabase
Gramene
Arizona Genomics Institute
Clemson Univ.
The Institute for Genomic Research (TIGR)
Plant Genome Initiative at Rutgers (PGIR)
Korea Rice Genome Research Program
riceweb
Rice Genetics Research
National Center for Gene Research Chinese Academy of Sciences
Rice Genome Project in Republic of China, Taiwan
France
Genoscope
National Center for Genetic Engineering and Biotechnology
Academia Sinica Plant Genome Center
Indian Initiative for Rice Genome Sequencing
Department of Biotechnology, India
Indian Agricultural Research Institute
International Rice Research Institute
International Rice Functional Genomics Consortium
Salk Institute Genomic Analysis Laboratory
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47. Database and Analysis tool

NIAS DNA Bank
Rice Genome Resource Center
DDBJ
ARS Genome Database Resource
NCBI
NCBI - Plant Genomes Central
NCGR
EBI
Protein Research Foundation
GENSCAN Web Server
Genome Software Development at the University of Washington
Rice insertion mutant database
Plant Promoter DB
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48. Genome Search Institute
National Institute of Agrobiological Sciences
Green Techno Project (Japanese)
The Institute for Genomic Research
Lawrence Berkeley National Laboratory
The Sanger Centre
Stanford Human Genome Center
Washington University Genome Sequencing Center
University of Washington Genome Center
Whitehead Institute/MIT
Human Genome Project Information
Human Genome Center Institute of Medical Science University of Tokyo
John Innes Centre - UK
Weizmann Institute Plant Genome Center
Cold Spring Harbor Laboratory
Stanford DNA Sequencing & Technology Center
Global Musa Genomics Consortium
Arabidopsis Genome Analysis
Maize Genome Database World Wide Web Server -->MaizeDB 6/28/2018 48

49. U. S. Wheat Genome Project
 The long term goal of this project is to decipher the chromosomal location
and biological function of all genes in the wheat (Triticum spp.) genomes.
 This knowledge will greatly enhance our understanding of the biology of the
wheat plant and create a new paradigm for the improvement of this
exceedingly important crop.
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52. GMOs( Genetic Modified Organism)
 A genetically modified organism (GMO) is any organism whose genetic material
has been altered using genetic engineering techniques (i.e., a
genetically engineered organism).
 GMOs are used to produce many medications and genetically modified foods and
are widely used in scientific research and the production of other goods.
 The term GMO is very close to the technical legal term, 'living modified organism',
defined in the Cartagena Protocol on Biosafety, which regulates international
trade in living GMOs (specifically, "any living organism that possesses a novel
combination of genetic material obtained through the use of modern
biotechnology")
 Transgenesis is the process of introducing a gene from another species — called a
transgene — into a living organism so that the organism exhibits a new property
and transmits that property to its offspring.
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53. History of GMOs
 Herbert Boyer and Stanley Cohen made the first genetically modified organism
(GMO) in 1973.
 They took a gene from a bacterium that provided resistance to the
antibiotic kanamycin, inserted it into a plasmid and then induced another bacteria
to uptake the plasmid.
 The bacteria was then able to survive in the presence of kanamycin.
 In 1974 Rudolf Jaenisch created a transgenic mouse by introducing foreign DNA
into its embryo, making it the world’s first transgenic animal.
 In 1983 the first genetically engineered plant was developed by Michael W.
Bevan, Richard B. Flavell and Mary-Dell Chilton.
 They infected tobacco with Agrobacterium transformed with an antibiotic
resistance gene and through tissue culture techniques were able to grow a new
plant containing the resistance gene.
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54. Cont…..
 The first genetically modified crop, an antibiotic-resistant tobacco plant, was
produced in 1982.
 China was the first country to commercialize transgenic plants, introducing a
virus-resistant tobacco in 1992.
 In 1994 Calgene attained approval to commercially release the Flavr Savr tomato,
the first genetically modified food.
 Also in 1994, the European Union approved tobacco engineered to be resistant to
the herbicide bromoxynil, making it the first genetically engineered crop
commercialized in Europe.
 An insect resistant Potato was approved for release in the US in 1995, and by 1996
approval had been granted to commercially grow 8 transgenic crops and one
flower crop (carnation) in 6 countries plus the EU.
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55. Tomato-(Flavr Savr)
 Flavr Savr (also known as CGN-89564-2; pronounced "flavor saver"), a genetically
modified tomato, was the first commercially grown genetically engineered food to
be granted a license for human consumption.
 It was produced by the Californian company Calgene, and submitted to the
U.S. Food and Drug Administration (FDA) in 1992.
 [1] On May 18, 1994,[2] the FDA completed its evaluation of the Flavr Savr tomato
and the use of APH(3')II, concluding that the tomato "is as safe as tomatoes bred
by conventional means" and "that the use of aminoglycoside 3'-phosphotransferase
II is safe for use as a processing aid in the development of new varieties of
tomato, rapeseed oil, and cotton intended for food use.“
 It was first sold in 1994, and was only available for a few years before production
ceased in 1997
 .[3] Calgene made history, but mounting costs prevented the company from
becoming profitable, and it was eventually acquired by Monsanto Company.
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56. Bt cotton
 Bt cotton is a genetically modified organism (GMO) or genetically modified
pest resistant plant cotton variety, which produces
an insecticide to bollworm.
 Bt cotton was first approved for field trials in the United States in 1993, and
first approved commercial use in the United States in 1995.
 Bt cotton was approved by the Chinese government in 1997.
 In 2002, a joint venture between Monsanto and Mahyco introduced Bt cotton
to India.
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57. Advantages of Bt cotton
 Bt cotton has several advantages over non-Bt cotton. The important advantages of
Bt cotton are briefly :
 Increases yield of cotton due to effective control of three types of bollworms, viz.
American, Spotted and Pink bollworms.
 Insects belonged to Lepidoptera (Bollworms) are sensitive to crystalline endotoxic
protein produced by Bt gene which in turn protects cotton from bollworms.
 Reduction in insecticide use in the cultivation of Bt cotton in which bollworms are
major pests.
 Reduction in environmental pollution by the use of insecticides.
 Bt cotton is ecofriendly and does not have adverse effect on parasites, predators,
beneficial insecticides and organisms present in soil.
 No health hazards due to rare use of insecticides (particularly who is engaged in
spraying of insecticides).
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58. Disadvantages of Bt cotton
 Bt cotton has some limitations
 High cost of Bt cotton seeds as compared to non Bt cotton seeds.
 Effectiveness up to 120 days, after that the toxin producing efficiency of the
Bt gene drastically reduces.
 Ineffective against sucking pests like jassids, aphids, whitefly etc.
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59. Cont…..
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WEBSITE FOR MAJOR CENTERS OF CROP RESEARCH

60. Cont…6/28/2018 60

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62. MaizeGDB
 MaizeGDB is a community-oriented, long-term, federally funded
informatics service to researchers focused on the crop plant and model
organism Zea mays.
 Tools of MaizeGDB-
 SNPversity
 SNPversity allows you to compare SNPs across a diverse selection of inbred
lines
 BLAST
 BLAST allows you to simultaneously BLAST datasets at many different
websites.
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63. MaizeGDB
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64. TAIR

The Arabidopsis Information Resource (TAIR) maintains a database of genetic
and molecular biology data for the model higher plant Arabidopsis thaliana .
 Data available from TAIR includes the complete genome sequence along with
gene structure, gene product information, gene expression, DNA and seed
stocks, genome maps, genetic and physical markers, publications, and
information about the Arabidopsis research community.
 Alexander Tairov (1885-1950), Russia
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66. Software for genome search
 Phred-
 The Phred quality values have been thoroughly tested for both accuracy and
power to discriminate between correct and incorrect base-calls.
 Phred quality score should be 20-30, Phred can use the quality values to
perform sequence trimming.
 Phred by developed by Dr. Phil Green Ewing, and is distributed by codon code
Washington.
 Phred is widely used by the largest academic and commercial DNAs
sequencing laboratories.
 This page gives a brief description of Phred for information about Phrap,
cross-match and Consed ,please visit – (www.phrap.com).
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67. Phrap-
 Phrap is a program for assembling shotgun DNA sequence data.
 Among other features, it allows use of the entire read and not just the
trimmed high quality part.
 It uses a combination of user-supplied and internally computed data quality
information to improve assembly accuracy in the presence of repeats.
 It constructs the contig sequence as a mosaic of the highest quality read
segments rather than a consensus.
 It provides extensive assembly information to assist in trouble-shooting
assembly problems, and it handles large datasets.
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68. Consed-
 Consed/Autofinish is a tool for viewing, editing, and finishing sequence
assemblies created with phrap.
 Finishing capabilities include allowing the user to pick primers and templates,
suggesting additional sequencing reactions to perform, and facilitating
checking the accuracy of the assembly using digest and forward/reverse pair
information.
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69. Cross-Match-
 Cross-Match is a general purpose utility for comparing any two DNA sequence
sets using a 'banded' version of swat.
 For example,
It can be used to compare a set of reads to a set of vector sequences and
produce vector-masked versions of the reads.
 A set of cDNA sequences to a set of cosmids, contig sequences found by two
alternative assembly procedures (for example, phrap and xbap) to each other,
or phrap contigs to the final edited cosmid sequence.
 It is slower but more sensitive than BLAST.
 See the phrap/cross-match/swat documentation and phrap documentation for
additional information.
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70. Staden Package
 It is Computer software
 The Staden Package is computer software, a set of tools for DNA sequence
assembly, editing, and sequence analysis.
 It is open-source software, released under a BSD 3-clause license.
 History-
 The Staden Package was developed by Rodger Staden's group at the Medical
Research Council (MRC) Laboratory of Molecular Biology, Cambridge, England,
since 1977.
 Stable release: 24 January 2012; 6 years ago
 Preview release: 25 April 2016; 23 months ago
 Original author(s): Rodger Staden
 License: BSD 3-clause
 Platforms: x86-32 (32 bit Intel x86), x86-64
 Written in: C, C++, Fortran, Tcl
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