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Mouse Gene Prediction Database

Zhang et. al. GENE EXPRESSION PROFILE SEARCH. Input name of gene for search. Common name or REFSEQ gi numbers. Examples: NM 026405.2 LOC210609 Map3k8. GO CATEGORY PREDICTION SEARCH. Choose a GO annotation category to view the genes predcited to be in this category:. Choose a GO Category:. SGO000001 cAMP metabolism, G protein sgnlng. SGO000002 complement activation, class. path. SGO000003 di , tri valent inorganic cation tn. SGO000005 (deoxyribo)nucleoside 2P metabolism. SGO000013 CNS brain development.

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Mouse Gene Prediction Database | mgpd.med.utoronto.ca Reviews

<META> DESCRIPTION

Zhang et. al. GENE EXPRESSION PROFILE SEARCH. Input name of gene for search. Common name or REFSEQ gi numbers. Examples: NM 026405.2 LOC210609 Map3k8. GO CATEGORY PREDICTION SEARCH. Choose a GO annotation category to view the genes predcited to be in this category:. Choose a GO Category:. SGO000001 cAMP metabolism, G protein sgnlng. SGO000002 complement activation, class. path. SGO000003 di , tri valent inorganic cation tn. SGO000005 (deoxyribo)nucleoside 2P metabolism. SGO000013 CNS brain development.

<META> KEYWORDS

1 hughes lab website

2 input gene

3 keyword search

4 sgo000004 chemosensory behavior

5 sgo000020 glycoprotein metabolism

6 sgo000064 carbohydrate transport

7 sgo000070 cellular morphogenesis

8 sgo000073 chromatin modification

9 sgo000082 cytokinin biosynthesis

10 precision

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hughes lab website,input gene,keyword search,sgo000004 chemosensory behavior,sgo000020 glycoprotein metabolism,sgo000064 carbohydrate transport,sgo000070 cellular morphogenesis,sgo000073 chromatin modification,sgo000082 cytokinin biosynthesis,precision

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Mouse Gene Prediction Database | mgpd.med.utoronto.ca Reviews

https://mgpd.med.utoronto.ca

Zhang et. al. GENE EXPRESSION PROFILE SEARCH. Input name of gene for search. Common name or REFSEQ gi numbers. Examples: NM 026405.2 LOC210609 Map3k8. GO CATEGORY PREDICTION SEARCH. Choose a GO annotation category to view the genes predcited to be in this category:. Choose a GO Category:. SGO000001 cAMP metabolism, G protein sgnlng. SGO000002 complement activation, class. path. SGO000003 di , tri valent inorganic cation tn. SGO000005 (deoxyribo)nucleoside 2P metabolism. SGO000013 CNS brain development.

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mgpd.med.utoronto.ca

1

BLAST Color schema description

http://mgpd.med.utoronto.ca/docs/color_schema.html

BLAST Color schema description. Masked regions in lower case. Everything else in upper case. Masked regions in lower case, gray letters. Unaligned regions in italic. Everything else in upper case. Masked regions in lower case, gray letters unless identity. Everything else in upper case. Unaligned regions in italic. Identity shown in red color. Similarity shown in blue color. Mismatches shown in black color. Masked regions in lower case, gray letters. Everything else in upper case.

2

Matrix and Gap Costs

http://mgpd.med.utoronto.ca/docs/matrix_info.html

Query length Substitution matrix Gap costs - - - - - - - - - - - - - - - - - - - - -. 85 BLOSUM-62 (11,1). Altschul, S.F. (1991) "Amino acid substitution matrices from an information theoretic perspective." J. Mol. Biol. 219:555-565. [2] States, D.J., Gish, W. and Altschul, S.F. (1991) "Improved sensitivity of nucleic acid database searches using application-specific scoring matrices." Methods 3:66-70. [3].

3

FASTA format description

http://mgpd.med.utoronto.ca/docs/fasta.html

A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (" ") symbol in the first column. It is recommended that all lines of text be shorter than 80 characters in length. An example sequence in FASTA. The nucleic acid codes supported are:. For those programs that use amino acid query sequences (BLASTP and TBLASTN), the accepted amino acid codes are:. A alanine P proline B aspartat...

4

BLAST search main parameters

http://mgpd.med.utoronto.ca/docs/newoptions.html

BLAST Search main parameters. Restricts the number of short descriptions of matching sequences reported to the number specified; default limit is 100 descriptions. See also EXPECT. The statistical significance threshold for including a sequence in the model used by PSI-BLAST on the next iteration. Enter the organism name in the form "Genus species" (e.g., "Homo sapiens"). A number of popular organism names are listed on a pull-down menu. Explore the taxonomy database at NCBI. It is not unusual for nothin...

5

BLAST search main parameters

http://mgpd.med.utoronto.ca/docs/options.html

BLAST Search main parameters. Display a histogram of scores for each search; default is yes. (See parameter H in the BLAST Manual). Restricts the number of short descriptions of matching sequences reported to the number specified; default limit is 100 descriptions. (See parameter V in the manual page). See also EXPECT and CUTOFF. Restrict a TBLASTN search to just the top or bottom strand of the database sequences; or restrict a BLASTN, BLASTX or TBLASTX search to just reading frames on the top or bottom ...

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hugheslab.ccbr.utoronto.ca

HughesData - Main - Hughes Lab

http://hugheslab.ccbr.utoronto.ca/twiki/bin/view/Main/HughesData

Yeast mRNA expression data. Mouse mRNA expression data. Yeast noncoding RNA data. Mouse noncoding RNA data. Other data types, tools, etc. Van Bakel et al., 2011, Genome Biology. The draft genome and transcriptome of Cannabis sativa.". Narasimhan et al., 2015, eLife. Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities.". Weirauch et al., 2014, Cell. Determination and inference of eukaryotic transcription factor sequence specificity.". Ray et al., 2013, Nature. Create...

hugheslab.med.utoronto.ca

HughesData - Main - Hughes Lab

http://hugheslab.med.utoronto.ca/twiki/bin/view/Main/HughesData

Yeast mRNA expression data. Mouse mRNA expression data. Yeast noncoding RNA data. Mouse noncoding RNA data. Other data types, tools, etc. Van Bakel et al., 2011, Genome Biology. The draft genome and transcriptome of Cannabis sativa.". Narasimhan et al., 2015, eLife. Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities.". Weirauch et al., 2014, Cell. Determination and inference of eukaryotic transcription factor sequence specificity.". Ray et al., 2013, Nature. Create...

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Mouse Gene Prediction Database

Zhang et. al. GENE EXPRESSION PROFILE SEARCH. Input name of gene for search. Common name or REFSEQ gi numbers. Examples: NM 026405.2 LOC210609 Map3k8. GO CATEGORY PREDICTION SEARCH. Choose a GO annotation category to view the genes predcited to be in this category:. Choose a GO Category:. SGO000001 cAMP metabolism, G protein sgnlng. SGO000002 complement activation, class. path. SGO000003 di , tri valent inorganic cation tn. SGO000005 (deoxyribo)nucleoside 2P metabolism. SGO000013 CNS brain development.

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mgpd.med.utoronto.ca

Mouse Gene Prediction Database

Zhang et. al. GENE EXPRESSION PROFILE SEARCH. Input name of gene for search. Common name or REFSEQ gi numbers. Examples: NM 026405.2 LOC210609 Map3k8. GO CATEGORY PREDICTION SEARCH. Choose a GO annotation category to view the genes predcited to be in this category:. Choose a GO Category:. SGO000001 cAMP metabolism, G protein sgnlng. SGO000002 complement activation, class. path. SGO000003 di , tri valent inorganic cation tn. SGO000005 (deoxyribo)nucleoside 2P metabolism. SGO000013 CNS brain development.

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