1. Online Counseling Resource YCMOU ELearning Drive… School of Architecture, Science and Technology Yashwantrao Chavan Maharashtra Open University, Nashik – 422222, India

2. Introduction Programmes and Courses SEP–SBI081–U01-CP1 OC-SEP–SBI081– CP1-02

3. School of Science and Technology, Online Counseling Resource… Credits  Academic Inputs by Sonali Alkari Faculty YCMOU Nagpur Centre, Faculty LAD college P.G. D of Biotechnology Research officer Ankur Seeds Pvt Ltd sonalisa_alkari@yahoo.co.in Sonalisaal@rediffmail.com © 2007, YCMOU. All Rights Reserved.

4. School of Science and Technology, Online Counseling Resource… © 2007, YCMOU. All Rights Reserved. How to Use This Resource  Counselor at each study center should use this presentation to deliver lecture of 40-60 minutes during Face-To-Face counseling.  Discussion about students difficulties or tutorial with assignments should follow the lecture for about 40-60 minutes.  Handouts (with 6 slides on each A4 size page) of this presentation should be provided to each student.  Each student should discuss on the discussion forum all the terms which could not be understood. This will improve his writing skills and enhance knowledge level about topics, which shall be immensely useful for end exam.  Appear several times, for all the Self-Tests, available for this course.  Student can use handouts for last minutes preparation just before end exam.

5. School of Science and Technology, Online Counseling Resource… © 2007, YCMOU. All Rights Reserved.5 Learning Objectives After studying this module, you should be able to: Describe Related data resources such as:  EST,  STS,  GSS,  HSS © 2007, YCMOU. All Rights Reserved.

6. School of Science and Technology, Online Counseling Resource… Expressed Sequence Tag-1  An expressed sequence tag or EST is a short sub- sequence of a transcribed spliced nucleotide sequence (either protein-coding or not).  They may be used to identify gene transcripts, and are instrumental in gene discovery and gene sequence determination.  The identification of ESTs has proceeded rapidly, with approximately 52 million ESTs now available in public databases (e.g. GenBank 5/2008, all species).  ESTs can be mapped to specific chromosome locations using physical mapping techniques, such as radiation hybrid mapping or FISH. © 2007, YCMOU. All Rights Reserved.

7. School of Science and Technology, Online Counseling Resource… Expressed Sequence Tag-2  An EST is produced by one-shot sequencing of a cloned mRNA (i.e. sequencing several hundred base pairs from an end of a cDNA clone taken from a cDNA library).  The resulting sequence is a relatively low quality fragment whose length is limited by current technology to approximately 500 to 800 nucleotides.  Because these clones consist of DNA that is complementary to mRNA, the ESTs represent portions of expressed genes.  They may be present in the database as either cDNA/mRNA sequence or as the reverse complement of the mRNA, the template strand. © 2007, YCMOU. All Rights Reserved.

8. School of Science and Technology, Online Counseling Resource… Expressed Sequence Tag-3  An Expressed Sequence Tag is a tiny portion of an entire gene, (usually 200- to 500-nucleotide-long, that are generated by sequencing either one or both ends of an expressed gene) that can be used to help identify unknown genes and to map their positions within a genome.  ESTs provide researchers with a quick and inexpensive route for discovering new genes, for obtaining data on gene expression and regulation, and for constructing genome maps.  Today, researchers using ESTs to study the human genome find themselves riding the crest of a wave of scientific discovery the likes of which has never been seen before. © 2007, YCMOU. All Rights Reserved.

9. School of Science and Technology, Online Counseling Resource… Expressed Sequence Tag-4  Expressed sequence tag are single-pass sequences of cDNA clones.  Databases of EST sequences are highly redundant but quite useful for gene identification.  There are many efforts to cluster EST sequences to remove the redundancy and low- quality sequences.  EST clusters in UniGene  Gene indexes at TIGR  EST clusters at Allgenes © 2007, YCMOU. All Rights Reserved.

10. School of Science and Technology, Online Counseling Resource… Expressed Sequence Tag-5 © 2007, YCMOU. All Rights Reserved.

11. School of Science and Technology, Online Counseling Resource… High Throughput Genome Sequence-1  The High Throughput Genomic (HTG) Sequences division was created to accommodate a growing need to make unfinished genomic sequence data rapidly available to the scientific community.  It was done in a coordinated effort among the International Nucleotide Sequence databases, DDBJ, EMBL, and GenBank. The HTG division contains unfinished DN  A sequences generated by the high-throughput sequencing centers. Sequence data in this division are available for BLAST homology searches against either the "htgs" database or the "month" database, which includes all new submissions for the prior month.  The HTG division of GenBank was described in a Genome Research article by Ouellette and Bogus. © 2007, YCMOU. All Rights Reserved.

12. School of Science and Technology, Online Counseling Resource… High Throughput Genome Sequence-2  High Throughput Genome Sequence is a term to distinguish all genomic sequence generated in a high- throughput manner.  In order to release data more rapidly, it became standard for all sequence centers to submit unfinished sequence into public repositories (the "Bermuda Rules").  This sequence is deposited into the HTG division of GenBank/EMBL/DDBJ.  In general, these terms are used to describe clone (BA/PAC/fosmid) based projects. keywords associated with HTGS:  HTGS_phase0: A project that has very light coverage, generally 1-2 fold coverage of the clone. This initial light coverage is produced to ensure that the clone is not redundant to other sequence. © 2007, YCMOU. All Rights Reserved.

13. School of Science and Technology, Online Counseling Resource… High Throughput Genome Sequence-3 HTGS_phase1: An unfinished project, usually representing 3-6 fold coverage of the clone. The fragments within the clone are not ordered or oriented with respect to each other. HTGS_phase2: An unfinished project, usually representing 5-10 fold coverage of the clone. The fragments within the clone are ordered and oriented. HTGS_phase3: A finished project. A single fragment of very high quality HTGS_draft: A draft project is either a phase 1 or phase 2 project that has exceeded a specified quality standard. © 2007, YCMOU. All Rights Reserved.

14. School of Science and Technology, Online Counseling Resource… High Throughput Genome Sequence-4  HTGS_fulltop: Added to a record when the center responsible for finishing the clone has added sufficient new shotgun coverage for their finishing process to begin.  HTGS_activefin: Added when the center responsible for finishing actually begins the process of finishing the sequence.  HTGS_cancelled: Added to clones that will never be finished. © 2007, YCMOU. All Rights Reserved.

15. School of Science and Technology, Online Counseling Resource… Sequence Tag Site-1  Sequence Tagged Sites (STS) markers have recently been developped in crop plants and more in trees.  A STS is a unique, simple-copy segment of the genome whose DNA sequence is known and which can be amplified by specific PCR.  When STS loci contain DNA length polymorphisms (e.g. simple sequence length polymorphisms, SSLPs), they become valuable genetic markers.  Sequence tagged sites that are derived from cDNAs (otherwise known as complementary DNAs) are called expressed sequence tags or EST.  The STS’ location and base sequence are known. © 2007, YCMOU. All Rights Reserved.

16. School of Science and Technology, Online Counseling Resource… Sequence Tag Site-2  In general, short sequences (200-500 bp) are produced throughout a genome. Oligonucleotide primers are generated such that this sequence can be amplified using PCR to produce a discrete band when analyzed by electrophoresis.  STS markers can be polymorphic or monomorphic.  They are critical to integrating non-sequence based maps (such as genetic or RH) with sequence based maps.  All STS sequences are incorporated into the STS Division of GenBank © 2007, YCMOU. All Rights Reserved.

17. School of Science and Technology, Online Counseling Resource… Sequence Tag Site-3  dbSTS is an NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites.  STS sequences can be submitted directly to GenBank submissions.  The dbSTS database offers an alternative route for submission of STS sequences to GenBank.  It is designed especially for the submission of large batches of STS sequences.  STS division entries in GenBank can be retrieved using Entrez. © 2007, YCMOU. All Rights Reserved.

18. School of Science and Technology, Online Counseling Resource… Sequence Tag Site-4  The STS division nucleotide sequences in FASTA format are available by anonymous FTP. Data files for UniSTS are also available at this site.  The STS division nucleotide sequences can be searched using BLAST.  STSs are useful for localizing and orienting the mapping and sequence data reported from many different laboratories and serve as landmarks on the developing physical map of the human genome © 2007, YCMOU. All Rights Reserved.

19. School of Science and Technology, Online Counseling Resource… Sequence Tag Site-5  The main advantage of STS loci lies in the speed with which they can be analyzed once PCR primer pairs have been identified.  Like RFLP loci, STS loci can be analyzed as co- dominance genetic markers and can in theory, be studied in member of the species or closely related species, provided that the DNA sequence is conserved at the PCR primer sites.  Analysis with STS markers thus combines the speed of the RAPD markers with the informativeness of RFLP markers. © 2007, YCMOU. All Rights Reserved.

20. School of Science and Technology, Online Counseling Resource… GSS: Genome Survey Sequences-1  The GSS division of GenBank is similar to the EST division, with the exception that most of the sequences are genomic in origin, rather than cDNA (mRNA).  In general, short sequences (200-500 bp) are produced throughout a genome.  It should be noted that two classes (exon trapped products and gene trapped products) may be derived via a cDNA intermediate.  Oligonucleotide primers are generated such that this sequence can be amplified using PCR to produce a discrete band when analyzed by electrophoresis. © 2007, YCMOU. All Rights Reserved.

21. School of Science and Technology, Online Counseling Resource… GSS: Genome Survey Sequences-2  Section 1.3.3 of the GenBank 96.0 release notes provides additional information about the GSS division.  Although dbGSS sequences are incorporated into the GSS Division of GenBank, annotation in dbGSS is more comprehensive and includes detailed information about the contributors, experimental conditions, and genetic map locations.  GSS sequences are also available as a flat file in the FASTA format by anonymous FTP in the /repository/dbGSS directory at ncbi.nlm.nih.gov © 2007, YCMOU. All Rights Reserved.

22. School of Science and Technology, Online Counseling Resource… GSS: Genome Survey Sequences-3 The GSS division contains (but is not limited to) the following types of data:  random "single pass read" genome survey sequences.  cosmid/BAC/YAC end sequences  exon trapped genomic sequences  Alu PCR sequences  transposon-tagged sequences © 2007, YCMOU. All Rights Reserved.

23. School of Science and Technology, Online Counseling Resource… What You Learn… You have learnt :  An expressed sequence tag or EST is a short sub- sequence of a transcribed spliced nucleotide sequence.  High Throughput Genome Sequence is a term to distinguish all genomic sequence generated in a high-throughput manner.  A STS is a unique, simple-copy segment of the genome whose DNA sequence is known and which can be amplified by specific PCR.  The GSS division of GenBank is similar to the EST division, with the exception that most of the sequences are genomic in origin, rather than cDNA (mRNA). © 2007, YCMOU. All Rights Reserved.

24. School of Science and Technology, Online Counseling Resource… Critical Thinking Questions 1.Describe the STS in details. 2.Write a short note on EST. 3.Describe GSS. 4.What is HTGS. © 2007, YCMOU. All Rights Reserved.24 © 2007, YCMOU. All Rights Reserved.

25. School of Science and Technology, Online Counseling Resource… Hints For Critical Thinking Question 1.Sequence Tagged Sites describe in details. 2.Expressed Sequence Tags Used to identify gene transcripts, and are instrumental in gene discovery and gene sequence determination. 3.Genome Survey Sequences. 4.High Throughput Genome Sequence © 2007, YCMOU. All Rights Reserved.25 © 2007, YCMOU. All Rights Reserved.

26. School of Science and Technology, Online Counseling Resource… Study Tips:1  Book1 Title: Principles of Genome Analysis And Genomics Author: Primrose, S.B. & Twyman, R.M. Publisher: Blackwell Publishing Company.  Book2 Title: Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins Author: Andreqas D. Baxevanis, B. F. Francis Ouellette Publisher: John Wiley and Sons, New York © 2007, YCMOU. All Rights Reserved.

27. School of Science and Technology, Online Counseling Resource… Study Tips:2  Book3 Title: Bioinformatics Sequence and Genome Analysis Author:David W. Mount. Publisher: Cold Spring Harborlaboratory Press.  Book4 Title: Bionformatics Concepts, Skills and Application Author: Rastogi, S.C., Mendiratta N, Rastogi, Publisher: CBS Publishers & Distributors © 2007, YCMOU. All Rights Reserved.

28. School of Science and Technology, Online Counseling Resource… Study Tips www.en.wikipedia.org Microsoft Encarta Encyclopedia http://en.wikipedia.org/wiki/ Wikipedia the free encyclopedia © 2007, YCMOU. All Rights Reserved.

29. School of Science and Technology, Online Counseling Resource… End of the Presentation Thank You © 2007, YCMOU. All Rights Reserved.