\ This track shows alignments between A. mellifera expressed sequence tags\ (ESTs) in GenBank and the genome that show signs of splicing when\ aligned against the genome. ESTs are single-read sequences, typically about \ 500 bases in length, that usually represent fragments of transcribed genes.\
\\ To be considered spliced, an EST must show \ evidence of at least one canonical intron, i.e. one that is at least\ 32 bases in length and has GT/AG ends. By requiring splicing, the level \ of contamination in the EST databases is drastically reduced\ at the expense of eliminating many genuine 3' ESTs.\ For a display of all ESTs (including unspliced), see the \ A. mellifera EST track.
\ \\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, darker shading\ indicates a larger number of aligned ESTs.
\\ The strand information (+/-) indicates the\ direction of the match between the EST and the matching\ genomic sequence. It bears no relationship to the direction\ of transcription of the RNA with which it might be associated.
\\ 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:\
\ This track may also be configured to display base labeling, a feature that\ allows the user to display all bases in the aligning sequence or only those \ that differ from the genomic sequence. For more information about this option,\ click \ here.\
\ \\ To make an EST, RNA is isolated from cells and reverse\ transcribed into cDNA. Typically, the cDNA is cloned\ into a plasmid vector and a read is taken from the 5'\ and/or 3' primer. For most — but not all — ESTs, the\ reverse transcription is primed by an oligo-dT, which\ hybridizes with the poly-A tail of mature mRNA. The\ reverse transcriptase may or may not make it to the 5'\ end of the mRNA, which may or may not be degraded.
\\ In general, the 3' ESTs mark the end of transcription\ reasonably well, but the 5' ESTs may end at any point\ within the transcript. Some of the newer cap-selected\ libraries cover transcription start reasonably well. Before the \ cap-selection techniques\ emerged, some projects used random rather than poly-A\ priming in an attempt to retrieve sequence distant from the\ 3' end. These projects were successful at this, but as\ a side effect also deposited sequences from unprocessed\ mRNA and perhaps even genomic sequences into the EST databases.\ Even outside of the random-primed projects, there is a\ degree of non-mRNA contamination. Because of this, a\ single unspliced EST should be viewed with considerable\ skepticism.
\\ To generate this track, A. mellifera ESTs from GenBank were aligned \ against the genome using blat. Note that the maximum intron length\ allowed by blat is 750,000 bases, which may eliminate some ESTs with very \ long introns that might otherwise align. When a single \ EST aligned in multiple places, the alignment having the \ highest base identity was identified. Only alignments having\ a base identity level within 0.5% of the best and at least 96% base identity \ with the genomic sequence are displayed in this track.
\ \\ This track was produced at UCSC from EST sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, \ Wheeler DL. \ GenBank: update. Nucleic Acids Res. \ 2004 Jan 1;32(Database issue):D23-6.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ rna 1 baseColorUseSequence genbank\ group rna\ indelDoubleInsert on\ indelQueryInsert on\ intronGap 30\ longLabel A. mellifera ESTs That Have Been Spliced\ priority 56\ shortLabel Spliced ESTs\ showDiffBasesAllScales .\ spectrum on\ track intronEst\ type psl est\ visibility dense\ est A. mel. ESTs psl est A. mellifera ESTs Including Unspliced 0 100 0 0 0 127 127 127 1 0 0\ This track shows alignments between A. mellifera expressed sequence tags\ (ESTs) in \ GenBank and the genome. ESTs are single-read sequences,\ typically about 500 bases in length, that usually represent fragments of\ transcribed genes.\
\ \\ 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 strand information (+/-) indicates the\ direction of the match between the EST and the matching\ genomic sequence. It bears no relationship to the direction\ of transcription of the RNA with which it might be associated.\
\ \\ 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:\
\ This track may also be configured to display base labeling, a feature that\ allows the user to display all bases in the aligning sequence or only those\ that differ from the genomic sequence. For more information about this option,\ go to the\ \ Base Coloring for Alignment Tracks page.\ Several types of alignment gap may also be colored;\ for more information, go to the\ \ Alignment Insertion/Deletion Display Options page.\
\ \\ To make an EST, RNA is isolated from cells and reverse\ transcribed into cDNA. Typically, the cDNA is cloned\ into a plasmid vector and a read is taken from the 5'\ and/or 3' primer. For most — but not all — ESTs, the\ reverse transcription is primed by an oligo-dT, which\ hybridizes with the poly-A tail of mature mRNA. The\ reverse transcriptase may or may not make it to the 5'\ end of the mRNA, which may or may not be degraded.\
\ \\ In general, the 3' ESTs mark the end of transcription\ reasonably well, but the 5' ESTs may end at any point\ within the transcript. Some of the newer cap-selected\ libraries cover transcription start reasonably well. Before the\ cap-selection techniques\ emerged, some projects used random rather than poly-A\ priming in an attempt to retrieve sequence distant from the\ 3' end. These projects were successful at this, but as\ a side effect also deposited sequences from unprocessed\ mRNA and perhaps even genomic sequences into the EST databases.\ Even outside of the random-primed projects, there is a\ degree of non-mRNA contamination. Because of this, a\ single unspliced EST should be viewed with considerable\ skepticism.\
\ \\ To generate this track, A. mellifera ESTs from GenBank were aligned\ against the genome using blat. Note that the maximum intron length\ allowed by blat is 750,000 bases, which may eliminate some ESTs with very\ long introns that might otherwise align. When a single\ EST aligned in multiple places, the alignment having the\ highest base identity was identified. Only alignments having\ a base identity level within 0.5% of the best and at least 96% base identity\ with the genomic sequence were kept.\
\ \\ This track was produced at UCSC from EST sequence data\ submitted to the international public sequence databases by\ scientists worldwide.\
\ \\
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.\
\
GenBank.\
Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42.\
PMID: 23193287; PMC:
\
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\
GenBank: update.\
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.\
PMID: 14681350; PMC:
\
Kent WJ.\
BLAT - the BLAST-like alignment tool.\
Genome Res. 2002 Apr;12(4):656-64.\
PMID: 11932250; PMC:
\ The mRNA track shows alignments between A. mellifera mRNAs\ in \ GenBank and the 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:\
\ This track may also be configured to display codon coloring, a feature that\ allows the user to quickly compare mRNAs against the genomic sequence. For more\ information about this option, go to the\ \ Codon and Base Coloring for Alignment Tracks page.\ Several types of alignment gap may also be colored;\ for more information, go to the\ \ Alignment Insertion/Deletion Display Options page.\
\ \\ GenBank A. mellifera mRNAs were aligned against the genome using the\ blat program. When a single mRNA aligned in multiple places,\ the alignment having the highest base identity was found.\ Only alignments having a base identity level within 0.5% of\ the best and at least 96% base identity with the genomic sequence were kept.\
\ \\ The mRNA track was produced at UCSC from mRNA sequence data\ submitted to the international public sequence databases by\ scientists worldwide.\
\ \\
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.\
\
GenBank.\
Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42.\
PMID: 23193287; PMC:
\
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\
GenBank: update.\
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.\
PMID: 14681350; PMC:
\
Kent WJ.\
BLAT - the BLAST-like alignment tool.\
Genome Res. 2002 Apr;12(4):656-64.\
PMID: 11932250; PMC:
\ This track shows the draft assembly of the A. mellifera genome. \ Whole-genome shotgun reads were assembled into contigs and when possible, \ contigs were grouped into scaffolds (also known as "supercontigs").\ The order, orientation and gap sizes between contigs within a scaffold are\ based on paired-end read evidence.
\\ In dense mode, this track depicts the contigs that make up the \ currently-viewed scaffold. \ Contig boundaries are distinguished by the use of alternating gold and brown \ coloration. Where gaps\ exist between contigs, spaces are shown between the gold and brown\ blocks. The relative order and orientation of the contigs\ within a scaffold is always known; therefore, a line is drawn in the graphical\ display to bridge the blocks.
\\ All components within this track are of fragment type "W"\ (Whole Genome Shotgun contig).
\ \ map 1 altColor 230,170,40\ color 150,100,30\ group map\ longLabel Assembly from Fragments\ shortLabel Assembly\ track gold\ type bed 3 +\ visibility hide\ augustusGene AUGUSTUS genePred AUGUSTUS ab initio gene predictions v3.1 0 100 12 105 0 133 180 127 0 0 0\ This track shows ab initio predictions from the program\ AUGUSTUS (version 3.1).\ The predictions are based on the genome sequence alone.\
\ \\ For more information on the different gene tracks, see our Genes FAQ.
\ \\ Statistical signal models were built for splice sites, branch-point\ patterns, translation start sites, and the poly-A signal.\ Furthermore, models were built for the sequence content of\ protein-coding and non-coding regions as well as for the length distributions\ of different exon and intron types. Detailed descriptions of most of these different models\ can be found in Mario Stanke's\ dissertation.\ This track shows the most likely gene structure according to a\ Semi-Markov Conditional Random Field model.\ Alternative splicing transcripts were obtained with\ a sampling algorithm (--alternatives-from-sampling=true --sample=100 --minexonintronprob=0.2\ --minmeanexonintronprob=0.5 --maxtracks=3 --temperature=2).\
\ \\ The different models used by Augustus were trained on a number of different species-specific\ gene sets, which included 1000-2000 training gene structures. The --species option allows\ one to choose the species used for training the models. Different training species were used\ for the --species option when generating these predictions for different groups of\ assemblies.\
| Assembly Group | \ \ \Training Species | \ \
| Fish | \ \ \zebrafish\ \ |
| Birds | \ \ \chicken\ \ |
| Human and all other vertebrates | \ \ \human\ \ |
| Nematodes | \ \ \caenorhabditis | \ \
| Drosophila | \ \ \fly | \ \
| A. mellifera | \ \ \honeybee1 | \ \
| A. gambiae | \ \ \culex | \ \
| S. cerevisiae | \ \ \saccharomyces | \ \
\ This table describes which training species was used for a particular group of assemblies.\ When available, the closest related training species was used.\
\ \\ Stanke M, Diekhans M, Baertsch R, Haussler D.\ \ Using native and syntenically mapped cDNA alignments to improve de novo gene finding.\ Bioinformatics. 2008 Mar 1;24(5):637-44.\ PMID: 18218656\
\ \\ Stanke M, Waack S.\ \ Gene prediction with a hidden Markov model and a new intron submodel.\ Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25.\ PMID: 14534192\
\ genes 1 baseColorDefault genomicCodons\ baseColorUseCds given\ color 12,105,0\ group genes\ longLabel AUGUSTUS ab initio gene predictions v3.1\ shortLabel AUGUSTUS\ track augustusGene\ type genePred\ visibility hide\ blastDm1FB D. mel. Proteins psl protein D. melanogaster Proteins (dm1) Mapped by Chained tBLASTn 1 100 0 0 0 127 127 127 0 0 0 http://flybase.bio.indiana.edu/.bin/fbidq.html?\ This track contains tBLASTn alignments of the peptides\ from the predicted and known genes identified in the D. melanogaster\ FlyBase as of 24 July 2004 to the A. mellifera sequence.\ \
\ First, predicted proteins from the D. melanogaster FlyBase track were\ aligned with the D. melanogaster genome using the blat program to \ discover exon boundaries. \ Next, the amino acid sequences that make up each exon were aligned with the \ A. mellifera sequence using the tBLASTn program.\ Finally, the putative A. mellifera exons were chained together using an \ organism-specific maximum gap size but no gap penalty. The single best exon \ chains extending over more than 60% of the query protein were included. Exon \ chains that extended over 60% of the query and matched at least 60% of the \ protein's amino acids were also included.\ \
\ tBLASTn is part of the NCBI Blast tool set. For more information on Blast, see\ Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ.\ Basic local alignment search tool.\ J Mol Biol. 1990 Oct 5;215(3):403-10.\ PMID: 2231712\
\ \\ Blat was written by Jim Kent. The remaining utilities \ required to produce this track were written by Jim Kent or Brian Raney.\ genes 1 blastRef dm1.blastFBRef00\ colorChromDefault off\ group genes\ longLabel D. melanogaster Proteins (dm1) Mapped by Chained tBLASTn\ pred dm1.blastFBPep00\ shortLabel D. mel. Proteins\ track blastDm1FB\ type psl protein\ url http://flybase.bio.indiana.edu/.bin/fbidq.html?\ visibility dense\ gap Gap bed 3 + Gap Locations 1 100 0 0 0 127 127 127 0 0 0
\ Gaps are represented as black boxes in this track.\ If the relative order and orientation of the contigs on either side\ of the gap is known, it is a bridged gap and a white line is drawn \ through the black box representing the gap. \
\\ All gaps in this assembly have type "fragment", i.e. gaps between the \ contigs of a draft clone.\
\ map 1 group map\ longLabel Gap Locations\ shortLabel Gap\ track gap\ type bed 3 +\ visibility dense\ gcPercent GC Percent bed 4 + Percentage GC in 20,000-Base Windows 0 100 0 0 0 127 127 127 1 0 0\ 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 group map\ longLabel Percentage GC in 20,000-Base Windows\ shortLabel GC Percent\ spectrum on\ track gcPercent\ type bed 4 +\ visibility hide\ genscan Genscan Genes genePred genscanPep Genscan Gene Predictions 0 100 170 100 0 212 177 127 0 0 0
\ This track shows predictions from the\ Genscan program\ written by Chris Burge.\ The predictions are based on transcriptional, translational and donor/acceptor\ splicing signals as well as the length and compositional distributions of exons,\ introns and intergenic regions.\
\ \\ For more information on the different gene tracks, see our Genes FAQ.
\ \\ This track follows the display conventions for\ gene prediction\ tracks.\
\ \\ The track description page offers the following filter and configuration\ options:\
\ For a description of the Genscan program and the model that underlies it,\ refer to Burge and Karlin (1997) in the References section below.\ The splice site models used are described in more detail in Burge (1998)\ below.\
\ \\ Burge C.\ Modeling Dependencies in Pre-mRNA Splicing Signals.\ In: Salzberg S, Searls D, Kasif S, editors.\ Computational Methods in Molecular Biology.\ Amsterdam: Elsevier Science; 1998. p. 127-163.\
\ \\ Burge C, Karlin S.\ \ Prediction of complete gene structures in human genomic DNA.\ J. Mol. Biol. 1997 Apr 25;268(1):78-94.\ PMID: 9149143\
\ genes 1 color 170,100,0\ group genes\ longLabel Genscan Gene Predictions\ shortLabel Genscan Genes\ track genscan\ type genePred genscanPep\ visibility hide\ microsat Microsatellite bed 4 Microsatellites - Di-nucleotide and Tri-nucleotide Repeats 0 100 0 0 0 127 127 127 0 0 0\ This track displays regions that are likely to be useful as microsatellite\ markers. These are sequences of at least 15 perfect di-nucleotide and \ tri-nucleotide repeats and tend to be highly polymorphic in the\ population.\
\ \\ The data shown in this track are a subset of the Simple Repeats track, \ selecting only those \ repeats of period 2 and 3, with 100% identity and no indels and with\ at least 15 copies of the repeat. The Simple Repeats track is\ created using the \ Tandem Repeats Finder. For more information about this \ program, see Benson (1999).
\ \\ Tandem Repeats Finder was written by \ Gary Benson.
\ \\
Benson G.\
\
Tandem repeats finder: a program to analyze DNA sequences.\
Nucleic Acids Res. 1999 Jan 15;27(2):573-80.\
PMID: 9862982; PMC:
\ This track shows known protein-coding and non-protein-coding genes \ for organisms other than A. mellifera, taken from the NCBI RNA reference \ sequences collection (RefSeq). The data underlying this track are \ updated weekly.
\ \\ This track follows the display conventions for \ gene prediction \ tracks.\ The color shading indicates the level of review the RefSeq record has \ undergone: predicted (light), provisional (medium), reviewed (dark).
\\ The item labels and display colors of features within this track can be\ configured through the controls at the top of the track description page. \
\ The RNAs were aligned against the A. mellifera genome using blat; those\ with an alignment of less than 15% were discarded. When a single RNA aligned \ in multiple places, the alignment having the highest base identity was \ identified. Only alignments having a base identity level within 0.5% of \ the best and at least 25% base identity with the genomic sequence were kept.\
\ \\ This track was produced at UCSC from RNA sequence data\ generated by scientists worldwide and curated by the \ NCBI RefSeq project.
\ \\
Kent WJ.\
\
BLAT--the BLAST-like alignment tool.\
Genome Res. 2002 Apr;12(4):656-64.\
PMID: 11932250; PMC:
\
Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J,\
Landrum MJ, McGarvey KM et al.\
\
RefSeq: an update on mammalian reference sequences.\
Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63.\
PMID: 24259432; PMC:
\
Pruitt KD, Tatusova T, Maglott DR.\
\
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.\
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.\
PMID: 15608248; PMC:
\ This track displays simple tandem repeats (possibly imperfect repeats) located\ by Tandem Repeats\ Finder (TRF) which is specialized for this purpose. These repeats can\ occur within coding regions of genes and may be quite\ polymorphic. Repeat expansions are sometimes associated with specific\ diseases.
\ \\ For more information about the TRF program, see Benson (1999).\
\ \\ TRF was written by \ Gary Benson.
\ \\
Benson G.\
\
Tandem repeats finder: a program to analyze DNA sequences.\
Nucleic Acids Res. 1999 Jan 15;27(2):573-80.\
PMID: 9862982; PMC:
\ This track shows D. melanogaster/A. mellifera genomic alignments using\ a gap scoring system that allows longer gaps than traditional\ affine gap scoring systems. It can also tolerate gaps in both D. melanogaster\ and A. mellifera simultaneously. These "double-sided"\ gaps can be caused by local inversions and overlapping deletions\ in both species. The D. melanogaster sequence is from the Apr. 2004 (BDGP R4/dm2) (dm2)\ assembly.
\\ 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 \ D. melanogaster assembly or an insertion in the A. mellifera 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 there are multiple \ chains over a particular portion of the A. mellifera genome, 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 D. melanogaster/A. mellifera\ split were removed, and the resulting abbreviated genomes were\ aligned with blastz. The transposons were then put back into the\ alignments. The resulting alignments were converted into axt format\ and the resulting axts fed into axtChain. AxtChain organizes all the \ alignments between a single D. melanogaster and a single A. mellifera chromosome\ 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 threshold were discarded; the remaining chains are\ displayed here.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his\ program RepeatMasker.
\\ 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 VB, Miller W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput. 2002:115-26.\ PMID: 11928468\
\ \\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
Evolution's cauldron: Duplication, deletion, and rearrangement\
in the mouse and human genomes.\
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.\
PMID: 14500911; PMC:
\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W.\
Human-Mouse Alignments with BLASTZ. \
Genome Res. 2003 Jan;13(1):103-7.\
PMID: 12529312; PMC:
\ This track shows the best D. melanogaster/A. mellifera \ chain for every part of the A. mellifera genome. It is useful for\ finding orthologous regions and for studying genome rearrangement.\ The D. melanogaster sequence used in this annotation is \ from the Apr. 2004 (BDGP R4/dm2) (dm2) 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.
\\ Lineage-specific repeats were identified by Arian Smit and his program \ RepeatMasker.
\\ The browser display and database storage of the nets were made\ by Robert Baertsch and Jim Kent.
\ \\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
Evolution's cauldron: Duplication, deletion, and rearrangement\
in the mouse and human genomes.\
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.\
PMID: 14500911; PMC:
\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W.\
Human-Mouse Alignments with BLASTZ.\
Genome Res. 2003 Jan;13(1):103-7.\
PMID: 12529312; PMC:
\
This track was created by using Arian Smit's
\ In full display mode, this track displays up to ten different classes of repeats:\
\ The level of color shading in the graphical display reflects the amount of \ base mismatch, base deletion, and base insertion associated with a repeat \ element. The higher the combined number of these, the lighter the shading.
\ \\ UCSC has used the most current versions of the RepeatMasker software \ and repeat libraries available to generate these data. Note that these \ versions may be newer than those that are publicly available on the Internet. \
\\ Data are generated using the RepeatMasker -s flag. Additional flags\ may be used for certain organisms. Repeats are soft-masked. Alignments may \ extend through repeats, but are not permitted to initiate in them. \ See the \ FAQ for \ more information.
\ \\ Thanks to Arian Smit and GIRI\ for providing the tools and repeat libraries used to generate this track.
\ \\ Jurka J.\ Repbase update: a database and an electronic journal of repetitive elements.\ Trends Genet. 2000 Sep;16(9):418-20.\ PMID: 10973072\
\ varRep 0 canPack off\ group varRep\ longLabel Repeating Elements by RepeatMasker\ priority 149.1\ shortLabel RepeatMasker\ spectrum on\ track rmsk\ type rmsk\ visibility dense\