BLAST Sequence Searching in Registry

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BLAST Sequence Searching in Registry

• Soichi Tokizane
• November 2002

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You will learn

• How sequences are represented in the Registry
  file today
• How to use BLAST for similarity searching
• Techniques for finding references to BLAST results

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Sequence Information from CAS
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CAS creates the Registry database
CAS Registry growth since 1965
Substances Registered (millions)
01
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CA has covered biochemistry journals and patents
since 1907
Oxidizing enzymes - (III) Specific nature of
tyrosinase and its action on products of
disintegration of protein compds. Arch.
Sci. phys. nat. gen. 24 1907
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Today, the CA database contains a very complete
bioscience collection
It covers

• Journals and patents from
• More than 3,000 bioscience titles
• Patents from 33 countries plus EP and WO
• Over 500 books and over 300 book series
• Conference proceedings
• Dissertations

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Over 40 of the 21.5 million bibliographic
records in CA cover bioscience information
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Biomolecules (sequences) are a major substance
class in REGISTRY
36 million substances
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Virtually all types of sequences are covered in
Registry

• Sequences from earlier literature
• Novel nucleic acid primers and probes
• Protein sequences deduced from gene translation
  and ESTs
• Sequences with uncommon or non-natural residues
• Chemically modified sequences
• Fusion proteins
• Genetically engineered sequences
• Protein nucleic acids (PNAs)

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BLAST Sequence Similarity Searching
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Registry offers several sequence search techniques

• BLAST similarity (homology) searching
• similarity searching is the retrieval of sequence
  matches based on identity, conservation, and gaps
• Sequence code match exact, family, motif,
  pattern
• Sequence name search

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BLAST is a similarity matching algorithm

• BLAST stands for Basic Local Alignment Search
  Tool
• Produced and offered by the U.S. National Center
  of Biotechnology Information (NCBI)
• Designed to quickly compare nucleic and amino
  acid sequences against desired databases

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Search Application
Find patent references for sequences similar to
the following recombinant human collagen. Conduct
a comprehensive search in Registry on STN.
MRAWIFFLLCLAGRALAAPLADYKDDDDKP GYLGGFLLVLHSQTDQEP
TCPLGMPRLWTG YSLLYLEGQEKAHNQDLGLAGSCLPVFSTL
HQVCHYAQRNDRSYWLASAAPLPRAWIFF MMPLSEEAIRPYVSRCAVC
EAPAQAVAVHS QDQSIPPCPQTWRSLWIGYSFLMHTGAGDQ
GGGQALMSPRAAPFLECQGRQGTLADY CHFFANKYSFWLTTVKADLQ
FSSAPAPDTL KESQAISRCQVCVKYS
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CAS Registry BLAST via STN on the Web is easy to
use

• 1. Install sequence plug-in
• 2. Conduct Registry BLAST similarity search
• 3. Search selected BLAST answers in STN to
  get the literature references

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BLAST is available via STN on the Web

• A plug-in must be downloaded and installed before
  using the BLAST module
• It is a one-time only requirement
• The plug-in is free
• Clicking on Get Sequence Plug-in takes you to
  easy-to-use Instructions

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Plug-in instruction page
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Conduct Registry BLAST Similarity Search
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Follow these steps for Registry BLAST searching

• Launch CAS Registry BLAST
• Submit sequence query
• Examine results and return to STN
• Continue searching in STN on the Web

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Logon to STN on the Web and select the Sequence
Assistant
1.
2.
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Select from one of three STN online options
before launch
Click on Launch button
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The main and new search windows appear

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Submit sequence query

• In a new session, the only available option is
  Similar Sequences
• Fast BLAST is available after the first search
• Click on the Similar Sequences button to open the
  Search by Sequence query page

Search by Sequence
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The Search by Sequence screen is easy to use
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Type in a result name

• Type desired name for sequence search
• Alpha or numeric
• Spaces and punctuation allowed
• STN will assign sequential number if you do not
  name the search
• The name can also be changed later in the Main
  Menu

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Recall Sequence is useful for re-submitting the
same query with different settings

• The most recently searched sequence is stored in
  a buffer that can be retrieved using this
  function
• This function is grayed out when you first begin

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Read from File allows you to upload directly from
a file

• The file can be
• A text file (e.g. .txt)
• In GCG or FASTA format
• An STN record (SQIDE display)

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The sequence query must be 1-letter code

• The sequence query can be
• Copied and pasted
• Read from File
• Typed directly
• a Recalled sequence
• The sequence length limit is 50,000 characters

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This screen is for inserting a sequence query
from file
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The BLAST program to be used is selected next
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Searches can be run on a subset of the Registry
File

• For proteins, the three options are
• The default is all CA sequences

Other options are available for nucleic acids,
such as include or exclude GenBank records.
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BLAST default settings are optimized

• Parameters can be modified
• Search sensitivity
• Low complexity filtering
• Maximum number of answers
• Show advanced options

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Advanced functions should only be modified with a
thorough understanding of BLAST principles

• Users are encouraged to contact bioinformatics
  departments for details, advice, and
  recommendations
• Additional information is also available at the
  NCBI Web page http//www.ncbi.nlm.nih.gov/

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The Main Window is for managing results

• The Main Window has columns for
• Assigned name
• Type of search
• Time created
• Status
• Results
• Reviewed status

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Results can be viewed once the search is complete

• The results are permanently stored on STN, until
  deleted by the user
• Old results can be reviewed when desired
• Up to 50 results sets can be stored

Highlight
Then view
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(No Transcript)
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Alignments can be viewed individually
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Alignments can be saved or printed
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The saved file has a summary of all the hits
and scores
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Select desired alignments for transfer to STN

• Check boxes
• Select by score category
• Select all

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Transfer RNs to STN

• Select Transfer RNs to STN
• Message indicates when the transfer is complete
• Log off the BLAST system -- Select Exit from File
  menu or close browser

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Retrieve RNs from BLAST

• The Sequence Assistant page appears after you
  exit BLAST
• Select the Retrieve RNs from BLAST option

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Return to STN on the Web

• STN will indicate if session is logged off
• If so, log on to STN on the Web
• Select Sequence Assistant
• Retrieve RNs from BLAST

To obtain a transcript of your session, you must
log in again.
Back to the STN on the Web login page
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Continue STN Searching
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L-Numbers are created from the automatic transfer
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L-Numbers are used for reference searches
These search results can be optionally combined
with DGENE, with routine use of STNs multifile
search interaction.
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STN Express with Discover! 6.01is now available
for Sequence Searching
http//www.cas.org/ONLINE/STN/interact/express.htm
l
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CAS REGISTRY BLAST is now searchable from Express
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Transferring BLAST data into an STN session is
seamlessly integrated into the software
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A report merges an STN transcript and BLAST
alignment data
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A report merges an STN transcript and BLAST
alignment data
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CAS REGISTRY BLAST will offer enhancements that
are in great demand by customers

• BLAST Alerts
• 1000 answers (increased from 200)
• Searching on lt50 residues
• BLAST version 2.2.3 from NCBI

These BLAST enhancements are also available
through STN on the Web new plug-in required.
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Setting up and managing CAS REGISTRY BLAST alerts
is easy
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Searches can now be set to retrieve only
sequences that have 50 residues or less--a big
help for primers and drug targets
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Summary
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In conclusion CAS Registry BLAST is necessary
for comprehensive sequence searching

• The Registry file is a key resource for
  biotechnology information
• CAS Registry BLAST provides a powerful and easy
  to use search engine
• BLAST RNs can be searched using STN on the Web or
  STN Express to get related patent and journal
  references
• Similarity searches in Registry can be combined
  with results from DGENE

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The End