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This document answers the following questions about the sequence summary report:

• When does a sequence summary report appear?
• What's in a sequence summary report?
• How do I use a sequence summary report?
• How do I view details for a single sequence?
• How do I download sequences in FASTA format?
• How do I forward sequences to MouseBLAST?
• How do the buttons work? What does Invert do?
• I got a summary report with a "Link to Results on FTP Site" message. What do I do now?
• I filled in fields on the Mouse Sequence Query Form and got this report. What does it tell me?
• I clicked a link on an MGI Marker Detail page and got this report. What does it tell me?
• I clicked a link on an MGI Reference Detail page and got this report. What does it tell me?
• What can I do with sequence summary report information?
• What does it mean if a value cannot be resolved to an MGI controlled vocabulary?

See also:

• MGI Glossary (unfamiliar terms or acronyms)
• Using the Mouse Sequence Query Form
• Using Sequence Detail Reports
• Sequence Query Hints
• MouseBLAST Help - Instructions for Using MouseBLAST

When does a sequence summary report appear?

A sequence summary report appears:

When you search for sequences...	For field details, see...
using the Web option in the Output Format field	I filled in fields on the Mouse Sequence Query Form...
from a Marker Detail report	I clicked a link on a Marker Detail page...
from on a Reference Detail report	I clicked a link on a Reference Detail page...

What's in a sequence summary report?

The Mouse Sequences Query Results summary report appears when you select either the Web or Web without toolbar option from the Output Format section of the Mouse Sequences Query Form. The summary report provides a general description of each sequence that your query returns. The report lists:

• Query parameters and sort options from the Mouse Sequence Query Form.
• 
  
• Number of matching sequences displayed in the report out of number found (e.g., 100 of 171 sequences displayed)
• 
  
• Summary information about the sequences matching your query, in columns. Depending on items checked in the Sorting and output format section of the sequences query form, columns headings can include Select (for your check marks) Sequence, Version, Type, Length, Strain/Species, Description from Sequence Provider, Source, Tissue, Library, Clone Collection, Marker Symbol, Marker Name, Map Position, Genome Coordinates. The default is to return sequence, type, length, strain/species, description, clone collection and marker symbol details.

You can select a sequence and view details (see Using Sequence Detail Reports), or you can download it in FASTA format or forward it to MouseBLAST.

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How do I use a sequence summary report?

There are several ways to use the summary reports. You can:

1. view sequence details for a single sequence by clicking either the MGI Sequence Detail or the provider (e.g., GenBank, RefSeq, and so on) link.
2. download one or more sequences in FASTA format.
3. forward one or more sequences to MouseBLAST.

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How do I view details for a single sequence?

You can elect to view the sequence details in the provider's database or in MGI.

1. Click the desired provider link (e.g., GenBank |EMBL |DDBJ).
   The provider's sequence record appears.
2. Click MGI Sequence Detail.
   The detail record for that sequence as stored in MGI appears. See Using Sequence Detail Reports.

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How do I download sequences in FASTA format?

To download sequences in FASTA format:

1. Click to put a check mark in the Select column next to one or more sequences.
2. Click the arrow next to For the selected sequences.
3. Click download in FASTA format.
4. Click GO.

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How do I forward sequences to MouseBLAST?

To forward sequences to MouseBLAST:

1. Click to put a check mark in the Select column next one or more sequences.
2. Click the arrow next to For the selected sequences.
3. Click forward to MouseBLAST.
4. Click GO.

For additional information, see:

• Using the Forward to MouseBLAST Form
• Interpreting the MouseBLAST Output Report

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I got a summary report with a "Link to Results on FTP Site" message. What do I do now?

The Mouse Sequence Summary Report with the FTP link summarizes your query parameters at the top of the page and beneath this, lists the number of items that matched your query.

• If you want to retrieve those matches right now, click the link (i.e., ftp://ftp.informatics.jax.org/wirequests/nnnnnn).
• If you want to access your results later, copy or save the URL to the MGI FTP site and make a note of how long they will be retained. If you don't retrieve your results within 72 hours, you'll have to rerun this query.

Example: FASTA summary report with link to MGI FTP site

Mouse Sequences
Query Results -- Summary

Query Summary
Type: equals RNA
Chromosome: on 2
Marker Symbol/Name: contains kit searching current symbols/names and synonyms.
Sort: by Type
71 of 71 sequences displayed
Link to Results on FTP Site

ftp://ftp.informatics.jax.org/pub/custom/generated/@22394.1/queryResults

Results will be available for 72 hours. Your results will be available until
05/09/2004 at 04:46 pm EDT.

Print or save this page to save the URL to your results.
Results Summary
20 of 20 sequences were successfully retrieved in FASTA format.

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How do the buttons work? What does Invert do?

Button	Action	Use this when...
Select all	Selects all the sequences on the list.	You want to examine every sequence.
Invert	A toggle switch. Removes any check marks and puts them in any boxes not previously selected.	the list of sequences you want to see is longer than the list you do not want to see. Click Select All, click the undesired sequences, click Invert. you don't want the action of Reset.
Reset	Removes any check marks from boxes.	You want to start over and make all new selections.
Go	Activates your choice (or the default) from the selection menu.	You are ready to download a sequence in FASTA format or forward it to MouseBLAST. See How do I download sequences in FASTA format? or How do I forward sequences to MouseBLAST? for details.

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I filled in fields on the Mouse Sequence Query Form and got this report. What does it tell me?

• At the top of the page is a list of the query parameters that produced this report.
• The table below identifies and provides information about the sequences matching your search criteria.
  
  

Examine this information, and, if it is not what you expect, return to the Query Form and change your parameters. See Sequence Query Hints for suggestions on how to do this.

• Click either MGI Sequence Detail or one of the provider links in the report to view sequence details.
• Select one or more sequences to download in FASTA format or forward to MouseBLAST. See FASTA or MouseBlast for details.

See What can I do with sequence summary report information? for more details.

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I clicked a link on a Marker Detail page and got this report. What does it tell me?

You were looking for sequences associated with a gene and clicked All Sequences from the Sequences section of a gene detail report.

Below the header of the Mouse Sequence Summary Report is the marker symbol, name, and ID, followed by the number of items displayed out of the number found.

The table provides information about the sequences associated with the marker. If a sequence is from the genome assembly, the coordinates appear in the Description from Sequence Provider column.

• Click either MGI Sequence Detail or one of the provider links in the report to view sequence details.
• Select one or more sequences to download in FASTA format or forward to MouseBLAST. See FASTA or MouseBlast for details.

See What can I do with sequence summary report information? for more details.

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I clicked a link on a Reference Detail page and got this report. What does it tell me?

You were looking for sequences associated with a reference and used the Sequences link on a Reference Detail report. The Sequence Summary report provides the J number and citation of the reference.

The table provides information about the sequences associated with the reference.

• Click either MGI Sequence Detail or one of the provider links in the report to view sequence details.
• Select one or more sequences to download in FASTA format or forward to MouseBLAST. See FASTA or MouseBlast for details.

See What can I do with sequence summary report information? for more details.

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What can I do with sequence summary report information?

After reviewing this information, you may want to run your query again, and change the...

• maximum number of items returned (for example, when the number of query results available is greater than the number appearing in your browser).
• columns to Show in results or the Sort by order of those results.
• output format (for example, to display tab-delimited text for use in a spreadsheet or FASTA format for use with a BLAST tool).
• query parameters so that you can narrow (or expand) your results. See Sequence Query Hints for suggestions on how to do this.

On the sequence summary report, you can follow links to:

• the MGI Sequence Detail page or the provider's sequence record
• an MGI Gene Detail page containing more information about the marker.

Depending on how you access this summary report and your sort choices, some or all of the following fields and links appear:

Select | Sequence | Version | Type | Length | Description from sequence provider | Strain | Tissue | Library | Marker symbol | Marker name | Map position | Genome Coordinates

Field	Description
Select	Check boxes for selecting sequences for downloading, or forwarding.
Sequence	Sequence identifier Name of the sequence provider, linked to the associated sequence in the provider's database. Link to the MGI sequence detail report
Version	Number assigned by the provider to this update of the sequence information. If blank, the provider does not furnish this information.
Type	Type of sequence: RNA, DNA, or polypeptide.
Length	Length of the sequence, in base pairs (RNA, DNA) or amino acids (polypeptides).
Description from Sequence Provider	Information about the sequence from the provider you selected (RefSeq, GenBank, and so on.)
Strain/Species	Mouse strain (or species if other than laboratory mouse) from which the sequence was derived. If the strain/species cannot be resolved to an MGI controlled vocabulary a message to this effect appears, marked with an asterisk. See What does it mean if a value cannot be resolved to an MGI controlled vocabulary?
Source Tissue	Mouse tissue from which the sequence was derived.
Library	Mouse library from which the sequence was derived.
Clone Collection	Name of clone collections from which the sequence was derived. (Not Applicable appears for RefSeq, UniProt, DFCI, DoTS, NIA sequences)
Marker Symbol	Gene/marker symbol associated with the sequence(s), linked to the MGI Gene Detail page.
Marker Name	Name of the gene/marker associated with the sequence.
Map Position	Chromosome(s) and cM position(s) of the markers each sequence is associated with.
Genome Coordinates	Assembly sequence coordinates for the mapped gene/marker. Format is Chromosome# (beginning coordinate - end coordinate)

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What does it mean if a value cannot be resolved to an MGI controlled vocabulary?

Providers describe sequence attributes (strains/species, tissues, libraries, clone collections, and so on) in their reports. MGI captures these original values, converts them to MGI controlled vocabularies if possible, and stores them in the MGI databases. Once captured, values are called resolved, and you can use them as search terms on the Mouse Sequence Query Form. If the original value is not resolved to a controlled vocabulary term, it does not produce results if queried upon; a message to this effect, marked with an asterisk, appears on your query report.

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