\ The GC percent track shows the percentage of G (guanine) and C (cytosine) bases\ in a 20,000 base window. Windows with high GC content are drawn more darkly \ than windows with low GC content. High GC content is typically associated with \ gene-rich areas.\
\\ This track was generated at UCSC.\ map 1 gbProtAnn GenBank Protein Annotations bed 4 + Proteins Annotated in GenBank NP_828849, Structual Analysis and Predictions 3 35 12 12 120 133 133 187 0 0 0
\ This track shows the locations of the putative proteins annotated \ in GenBank as \ \ NP_828849 (21-APR-2003, NP_828849.1 GI:29836505).
\ \ \\ (From the GenBank entry):
\ \\ Method: conceptual translation.
\\ Note: It was assumed that the SARS orf1ab polyprotein processing map\ should be similar to that of murine hepatitis virus. However, of the\ two MHV papain-like proteinases, only PLP-2 seems to be well conserved\ for SARS coronavirus. The putative mature peptides located downstream\ from nsp1 are probably cleaved from the polyprotein by the nsp2\ proteinase (3CL-PRO). The preliminary annotation of\ putative proteins and mature peptides was conducted at the NCBI.
\\ Also note: There is a putative frameshift of -1 at genomic coord 13383 \ (protein base 4379).
\ \ \\ The information was submitted to \ NCBI\ GenBank by \ \ BCCA Genome Sciences Centre, British Columbia Centre for Disease\ Control and National Microbiology Laboratory Canada\ .
\ \ \ genes 1 softberryGene Fgenesv+ Genes genePred softberryPep Fgenesv+ Gene Predictions 3 48 0 100 0 127 177 127 0 0 0\ Fgenesv+ predictions are based on Softberry's gene-finding software for viral genomes.
\ \\ The Fgenesv gene prediction algorithm is based on pattern recognition of \ different types of signals and Markov chain models of coding regions. The \ optimal combination of these features is found by dynamic programming; a \ set of gene models is constructed along the given sequence. Fgenesv+ is the \ Softberry automatic annotation pipeline that uses the Fgenesv gene predictor \ and annotations of predicted proteins, comparing them with protein databases.\ For more information, see \ Softberry's Fgenesv web page.
\ \\ The Fgenesv+ gene predictions were produced by \ Softberry Inc. Thanks to\ Victor Solovyev for providing these data.
\ \ genes 1 all_mrna $Organism mRNAs psl . $Organism mRNAs from GenBank 3 54 0 0 0 127 127 127 1 0 0\ This track shows alignments between viral mRNAs\ in GenBank and the SARS draft sequence.
\ \\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, the items that\ are more darkly shaded indicate matches of better quality.
\\ The description page for this track has a filter that can be used to change \ the display mode, alter the color, and include/exclude a subset of items \ within the track. This may be helpful when many items are shown in the track \ display, especially when only some are relevant to the current task.
\\ To use the filter:\
\ GenBank viral mRNAs were aligned against the SARS draft sequence using the\ blat program (translated alignments). \ These alignments were not filtered (as they usually would be \ for vertebrate genomes) because of the rapid evolution of viruses and the\ greater variance.
\ \\ This track was produced at UCSC from mRNA sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and\ Wheeler, D.L.\ GenBank: update. Nucleic Acids Res. 32,\ D23-6 (2004).
\\ Kent, W.J.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 12(4), 656-664 (2002).
\ \ rna 1 baseColorDefault diffCodons\ baseColorUseCds genbank\ baseColorUseSequence genbank\ indelDoubleInsert on\ indelPolyA on\ indelQueryInsert on\ showDiffBasesAllScales .\ xenoMrna Viral mRNAs psl xeno All Viral mRNAs from GenBank Using Blastz 3 55 0 0 0 127 127 127 1 0 0\ The Viral mRNA track shows alignments between viral mRNAs\ in GenBank and the SARS genome.
\ \\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, the items that\ are more darkly shaded indicate matches of better quality.
\\ The description page for this track has a filter that can be used to change \ the display mode, alter the color, and include/exclude a subset of items \ within the track. This may be helpful when many items are shown in the track \ display, especially when only some are relevant to the current task.
\\ To use the filter:\
\ GenBank Viral mRNAs were aligned against the genome using the \ blastz program. When a single mRNA aligned in multiple places, \ the alignment having the highest base identity was found. \ Only those alignments having at least 60% base identity were kept.
\ \\ This track was produced at UCSC from mRNA sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and\ Wheeler, D.L.\ GenBank: update. Nucleic Acids Res. 32,\ D23-6 (2004).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-mouse alignments with BLASTZ.\ Genome Res. 13(1), 103-107 (2003).
\ rna 1 baseColorUseCds genbank\ baseColorUseSequence genbank\ indelDoubleInsert on\ indelQueryInsert on\ showDiffBasesAllScales .\ xenoBlastzMrna Viral mRNAs Chained psl xeno All Viral mRNAs from GenBank Using Blastz Chained 3 55 0 0 0 127 127 127 1 0 0\ The Viral mRNA track shows alignments between viral mRNAs\ in GenBank and the SARS genome.
\ \\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, the items that\ are more darkly shaded indicate matches of better quality.
\ \\ GenBank viral mRNAs were aligned against the genome using the \ blastz program. When a single mRNA aligned multiple places, \ the alignment having the highest base identity was found. \ Only those alignments having at least 60% base identity were kept.\ These alignments were converted into axt format and the \ resulting axts fed into axtChain. AxtChain organizes all the \ alignments between a single viral mrna and the SARS genome into a group, \ and makes a kd-tree out of all the gapless subsections (blocks) of the \ alignments. Next, maximally scoring chains of these blocks were found by \ running a dynamic program over the kd-tree. Chains scoring below a \ certain threshold were discarded; the remaining chains are displayed in\ this track.
\ \\ This track was produced at UCSC from mRNA sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and \ Wheeler, D.L. \ GenBank: update. Nucleic Acids Res. 32,\ D23-6 (2004).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-mouse alignments with BLASTZ.\ Genome Res. 13(1), 103-107 (2003).
\ \ rna 1 otherSARS Other SARS psl . Other SARS Coronavirus (Partial or Complete) 3 132 75 75 120 165 165 187 0 0 0 http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$$\ The following sequences were retrieved from NCBI on April 25, 2003, \ and aligned to the SARS coronavirus TOR2 using \ blat:\ \
In details page view, you may click on the link in the Alignment Summary section to see a detailed\ view of the alignment.
\ \ compGeno 1 viralProt Coronavirus Proteins psl . Coronavirus Proteins from Swissprot at least 67% ID Using Blat 3 133 0 0 0 127 127 127 0 0 0 http://us.expasy.org/cgi-bin/niceprot.pl?$$\ The $Organism mRNA track shows alignments between viral proteins\ in SwissProt and the $Organism draft sequence. Aligning regions (usually exons)\ are shown as black boxes connected by lines for gaps (spliced\ out introns usually). In full display, arrows on the introns\ indicate the direction of transcription.
\ \\ Swissprot coronavirus proteins are aligned against the $Organism draft sequence using the \ BLAT program (translated alignments). \ These alignments are filtered for alignments greater than 67% (as they usually would be \ for vertebrate genomes) because viruses evolve so quickly and there \ is much greater variance.
\ \\ The $Organism viral protein track is produced at UCSC from protein sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ compGeno 1