\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \ \By default, the chains to chromosome-based assemblies are colored\ based on which chromosome they map to in the aligning organism. To turn\ off the coloring, check the "off" button next to: Color\ track based on chromosome.
\\ To display only the chains of one chromosome in the aligning\ organism, enter the name of that chromosome (e.g. chr4) in box next to: \ Filter by chromosome.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz using dynmamic masking, and the transposons were then \ added back in. The resulting alignments were converted into psl format \ using the lavToPsl program. The axt alignments were fed into axtChain, which \ organizes all alignments between a single $o_organism chromosome and a \ single $organism chromosome into a group and creates a kd-tree out of the \ gapless subsections (blocks) of the alignments. A dynamic program was then \ run over the kd-trees to find the maximally scoring chains of these blocks.\ \ $matrix\ \ Chains scoring below a threshold of 2000 were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Repeat areas we marked in the genome with WindowMasker as\ developed by: Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ 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), 103-7 (2003).
\\ Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\ WindowMasker: window-based masker for sequenced genomes. \ Bioinformatics. 2006 Jan 15;22(2):134-41. Epub 2005 Nov 15.
\ \ compGeno 1 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\ matrixHeader A, C, G, T\ otherDb caeJap1\ chainCaePb2 $o_Organism Chain chain caePb2 $o_Organism ($o_date/$o_db) Chained Alignments 0 130 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \ \By default, the chains to chromosome-based assemblies are colored\ based on which chromosome they map to in the aligning organism. To turn\ off the coloring, check the "off" button next to: Color\ track based on chromosome.
\\ To display only the chains of one chromosome in the aligning\ organism, enter the name of that chromosome (e.g. chr4) in box next to: \ Filter by chromosome.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz using dynmamic masking, and the transposons were then \ added back in. The resulting alignments were converted into psl format \ using the lavToPsl program. The axt alignments were fed into axtChain, which \ organizes all alignments between a single $o_organism chromosome and a \ single $organism chromosome into a group and creates a kd-tree out of the \ gapless subsections (blocks) of the alignments. A dynamic program was then \ run over the kd-trees to find the maximally scoring chains of these blocks.\ \ $matrix\ \ Chains scoring below a threshold of 2000 were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Repeat areas we marked in the genome with WindowMasker as\ developed by: Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ 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), 103-7 (2003).
\\ Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\ WindowMasker: window-based masker for sequenced genomes. \ Bioinformatics. 2006 Jan 15;22(2):134-41. Epub 2005 Nov 15.
\ \ compGeno 1 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\ matrixHeader A, C, G, T\ otherDb caePb2\ chainCaeRem3 $o_Organism Chain chain caeRem3 $o_Organism ($o_date/$o_db) Chained Alignments 0 128 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \ \By default, the chains to chromosome-based assemblies are colored\ based on which chromosome they map to in the aligning organism. To turn\ off the coloring, check the "off" button next to: Color\ track based on chromosome.
\\ To display only the chains of one chromosome in the aligning\ organism, enter the name of that chromosome (e.g. chr4) in box next to: \ Filter by chromosome.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz using dynmamic masking, and the transposons were then \ added back in. The resulting alignments were converted into psl format \ using the lavToPsl program. The axt alignments were fed into axtChain, which \ organizes all alignments between a single $o_organism chromosome and a \ single $organism chromosome into a group and creates a kd-tree out of the \ gapless subsections (blocks) of the alignments. A dynamic program was then \ run over the kd-trees to find the maximally scoring chains of these blocks.\ \ $matrix\ \ Chains scoring below a threshold of 2000 were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Repeat areas we marked in the genome with WindowMasker as\ developed by: Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ 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), 103-7 (2003).
\\ Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\ WindowMasker: window-based masker for sequenced genomes. \ Bioinformatics. 2006 Jan 15;22(2):134-41. Epub 2005 Nov 15.
\ \ compGeno 1 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\ matrixHeader A, C, G, T\ otherDb caeRem3\ chainCb3 $o_Organism Chain chain cb3 $o_Organism ($o_date/$o_db) Chained Alignments 0 126 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \ \By default, the chains to chromosome-based assemblies are colored\ based on which chromosome they map to in the aligning organism. To turn\ off the coloring, check the "off" button next to: Color\ track based on chromosome.
\\ To display only the chains of one chromosome in the aligning\ organism, enter the name of that chromosome (e.g. chr4) in box next to: \ Filter by chromosome.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz using dynmamic masking, and the transposons were then \ added back in. The resulting alignments were converted into psl format \ using the lavToPsl program. The axt alignments were fed into axtChain, which \ organizes all alignments between a single $o_organism chromosome and a \ single $organism chromosome into a group and creates a kd-tree out of the \ gapless subsections (blocks) of the alignments. A dynamic program was then \ run over the kd-trees to find the maximally scoring chains of these blocks.\ \ $matrix\ \ Chains scoring below a threshold of 2000 were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Repeat areas we marked in the genome with WindowMasker as\ developed by: Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ 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), 103-7 (2003).
\\ Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\ WindowMasker: window-based masker for sequenced genomes. \ Bioinformatics. 2006 Jan 15;22(2):134-41. Epub 2005 Nov 15.
\ \ compGeno 1 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\ matrixHeader A, C, G, T\ otherDb cb3\ chainPriPac1 $o_Organism Chain chain priPac1 $o_Organism ($o_date/$o_db) Chained Alignments 0 122 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \ \By default, the chains to chromosome-based assemblies are colored\ based on which chromosome they map to in the aligning organism. To turn\ off the coloring, check the "off" button next to: Color\ track based on chromosome.
\\ To display only the chains of one chromosome in the aligning\ organism, enter the name of that chromosome (e.g. chr4) in box next to: \ Filter by chromosome.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz using dynmamic masking, and the transposons were then \ added back in. The resulting alignments were converted into psl format \ using the lavToPsl program. The axt alignments were fed into axtChain, which \ organizes all alignments between a single $o_organism chromosome and a \ single $organism chromosome into a group and creates a kd-tree out of the \ gapless subsections (blocks) of the alignments. A dynamic program was then \ run over the kd-trees to find the maximally scoring chains of these blocks.\ \ $matrix\ \ Chains scoring below a threshold of 2000 were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Repeat areas we marked in the genome with WindowMasker as\ developed by: Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ 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), 103-7 (2003).
\\ Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\ WindowMasker: window-based masker for sequenced genomes. \ Bioinformatics. 2006 Jan 15;22(2):134-41. Epub 2005 Nov 15.
\ \ compGeno 1 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\ matrixHeader A, C, G, T\ otherDb priPac1\ multiz6way Conservation wigMaf 0.0 1.0 Multiz Alignment & Conservation (6 nematodes) 3 104.2 0 10 100 0 90 10 0 0 0 compGeno 1 autoScaleDefault Off\ frames multiz6wayFrames\ irows on\ maxHeightPixels 100:40:11\ pairwiseHeight 12\ spanList 1\ speciesCodonDefault ce5\ speciesOrder caeRem3 cb3 caePb2 caeJap1 priPac1\ summary multiz6waySummary\ treeImage phylo/ce5_6way.gif\ wiggle phastCons6way\ windowingFunction mean\ yLineOnOff Off\ netCaeJap1 $o_Organism Net netAlign caeJap1 chainCaeJap1 $o_Organism ($o_date/$o_db) Alignment Net 1 125 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ The browser display and database storage of the nets were made\ by Robert Baertsch and Jim Kent.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA. 2003;100(20):11484-11489.
\\ Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R,\ Haussler D, Miller W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 2003 Jan;13(1):103-7.
\ compGeno 0 otherDb caeJap1\ netCaePb2 $o_Organism Net netAlign caePb2 chainCaePb2 $o_Organism ($o_date/$o_db) Alignment Net 1 131 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ The browser display and database storage of the nets were made\ by Robert Baertsch and Jim Kent.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA. 2003;100(20):11484-11489.
\\ Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R,\ Haussler D, Miller W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 2003 Jan;13(1):103-7.
\ compGeno 0 otherDb caePb2\ netCaeRem3 $o_Organism Net netAlign caeRem3 chainCaeRem3 $o_Organism ($o_date/$o_db) Alignment Net 1 129 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ The browser display and database storage of the nets were made\ by Robert Baertsch and Jim Kent.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA. 2003;100(20):11484-11489.
\\ Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R,\ Haussler D, Miller W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 2003 Jan;13(1):103-7.
\ compGeno 0 otherDb caeRem3\ netCb3 $o_Organism Net netAlign cb3 chainCb3 $o_Organism ($o_date/$o_db) Alignment Net 1 127 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ The browser display and database storage of the nets were made\ by Robert Baertsch and Jim Kent.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA. 2003;100(20):11484-11489.
\\ Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R,\ Haussler D, Miller W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 2003 Jan;13(1):103-7.
\ compGeno 0 otherDb cb3\ netPriPac1 $o_Organism Net netAlign priPac1 chainPriPac1 $o_Organism ($o_date/$o_db) Alignment Net 1 123 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ The browser display and database storage of the nets were made\ by Robert Baertsch and Jim Kent.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA. 2003;100(20):11484-11489.
\\ Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R,\ Haussler D, Miller W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 2003 Jan;13(1):103-7.
\ compGeno 0 otherDb priPac1\