Chip Library File (1LQ) by nkc8ft

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                  Chip Library File (1LQ)
                            Specification




Author            Xue Mei Zhou

Revision          V2.0

Date              4/19/04




Print Name        Signature Approvals           Date    Department
Xue Mei Zhou                                            Chip Design Operations

Gloria Cheung                                           Chip Design

Mike Mittmann                                           Chip Design

Bill Kurani                                             Quality Assurance
                                                                    Chip Library File (1LQ), V2.0
                                                             Chip Library File Format Specification



                                   Revision History

Revision   Date        Prepared by         Change/Reason Summary
1          1/4/00      J. Retief           Initial Version

2          4/19/04     XM Zhou             Correction to Destype direction; first two header lines
                                           are optional; formatting changes




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                                                                                                                        Chip Library File (1LQ), V2.0
                                                                                                                 Chip Library File Format Specification


                                                          Table of Contents
1     INTRODUCTION ...............................................................................................................................................4
    1.1      PURPOSE .........................................................................................................................................................4
    1.2      AUDIENCE ......................................................................................................................................................4
    1.3      SCOPE .............................................................................................................................................................4
2     1LQ FILE .............................................................................................................................................................4
    2.1      1ST TWO HEADER LINES ..................................................................................................................................4
    2.2      MAIN FILE ......................................................................................................................................................4




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                                                                             Chip Library File (1LQ), V2.0
                                                                      Chip Library File Format Specification

1     INTRODUCTION

1.1    Purpose
This document describes the general format and the syntax for the Chip Library file (1LQ).

1.2    Audience
The intended audience of this document includes the following groups:
 Chip Design Operations
 Chip Design Development
 Chip Design Test
 Quality Assurance

1.3    Scope
The 1LQ file is generally for internal use and may be available to customers should they require more
information not contained in the CDF file.

2     1LQ File
The 1LQ file is a tab delimited text file. Blank lines are not allowed anywhere within the file. Each column
must contain a value. The same (X,Y) values may be duplicated multiple times to represent virtual
probes.

2.1    1st Two Header Lines
The first line specifies the number of rows and columns contained within the 1LQ file. The format of this
line is:
         COLS/ROWS=<XGrid><TAB><YGrid><TAB>Dummy
For example:
         COLS/ROWS=126            126     Dummy

The second line is a dummy line. Both header headers may be omitted.

2.2    Main File
The main file starts with a tab delimited header line, followed by the actual records.

 Column Heading         Type       Max       Description
                                   Length
 X                      integer              X coordinate (>=0 and <= maximum XGrid)
 Y                      integer              Y coordinate (>=0 and <= maximum YGrid)
 SEQUENCE               string     255       Probe sequence (string of “A”, “C”, “G”, or “T”) tiled at the (X,
                                             Y) location specified in 3’-5’ direction. “!” is used to denote
                                             blank probe.
 DESTYPE                integer              Design type for a given probe.
                                             +        probe for sense target
                                             -        probe for antisense target

                                             The following absolute values are acceptable:
                                             0        blank probe
                                             1        generic probe (used for Text and Center Cross)
                                             2        primer (primers to amplicons)
                                             3        thermodynamic control (corner checkerboards)
                                             4        edge control
                                             6        horizontal or vertical bar
                                             7        normalization grid



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                                                                       Chip Library File (1LQ), V2.0
                                                                Chip Library File Format Specification

 Column Heading     Type      Max      Description
                              Length
                                       10      user qc (synt check / QC)
                                       11      automated synthesis check “extended”
                                       12      automated synthesis check “local”
                                       13      automated synthesis check “poly”: AAA, CCC etc.
                                       14      cycle fidelity probe

                                       111      perfect match (PM) expression & mapping probe
                                       113      mismatch (MM) expression & mapping probe
                                       102      perfect match (PM) resequencing probe
                                       103      mismatch (MM) resequencing probe
 FEATURE            string    9        “control” – not used
 QUALIFIER          string    32       Name of the probe set; set to “default” is this is a control or
                                       blank probe.
 EXPOS              long               Interrogation position relative to the target.
 PLEN               integer            Probe length. It should agree with the Length (SEQUENCE)
                                       value.
 POS                integer            Interrogation position relative to the Probe Sequence.
 CBASE              string    1        Complementary Base; same as TBase.
 PBASE              string    1        Base in probe at interrogation position; set to “!” for blank
                                       probe.
 TBASE              string    1        Base in target at interrogation position; set to “!” for blank
                                       probe.
 IPBASE             string    1        Complement of PBase.
 UNIT               long               A unique number for each probe set. Generally, there is a 1-
                                       1 relationship between probe set name and unit. For
                                       resequencing designs, all sense probes have unit=1 and all
                                       antisense probes have unit=2.
 BLOCK              integer            -1 for unit=-1; 0 for all other unit values. This field is not
                                       used.
 ATOM               integer            A unique number identifying each perfect match probe and
                                       its corresponding mismatch probe(s) within a probe set.




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