NOTE: These new files are not yet supported by version 2.2 of the AllGenes site. We anticipate updating the AllGenes site by the end of August, 2001. (mus|hum)DoTS_.seq.gz: Fasta formatted sequence file with the DoTS identifier at the beginning of the defline. You can link back to AllGenes.org using this identifer. eg. for >DT.118717. http://www.allgenes.org/gc/servlet?page=rna&id=DT.118717 (mus|hum)DoTS_AssSeqIds_.dat.gz: lists the GenBank accessions of the sequences contained in the associated DoTS assembly. A ".1" has been appended to those accessions that represent mRNA sequences. NOTE: this is NOT the version which NCBI has recently adopted but rather a simple means of identifying those sequences that represent mRNA entries. musDOTS_Proteins_06_27_01.tar contains 2 zipped files with proteins derived from non-singleton assemblies: 30329 entries, good_nonsingles.pep, and from singletons: 56785 entries, good_singletons.pep. Both sets comprise sequences with cutoff p_value <0.2 musDoTS_Proteins_Update_08_15_01.tar contains 5 files for musDOTS_Proteins_06_27_01.tar update. These are To_be_deleted_section: 1214 - nonsingleton entries; 5074 - singleton entries; Novel: 1723 -new (including 625 updated) non-singletons; 525 - new singletons; musDoTS.Singletons.acc, musDoTS.Nonsingles.acc - contain two columns: aa_sequence_id na_sequence_id for musDOTS_Proteins_06_27_01.tar, good_singletons.pep, good_nonsingles.pep, correspondingly for linking to AllGenes assembly via url: http://www.cbil.upenn.edu/servlet/allgenes-dev/servlet?page=rna&id=DT. humDoTS_Proteins_10_10_01.tar contains 2 files: Singletons.fasta (156404 entries), Nonsingles.fasta (67817 entries) in fasta format A Fasta header contains five fields: na_sequence_id, aa_sequence_id, join() with segments, translation_score (from framefinder, in case of trivial translation value is -999), (translation_score is highly correlated with the length of a protein, so it could be taken that way) p_value (it is the chance probability to get ORF on this length or longer given the length of initial assembly. Smaller p_values corr- respond to longer proteins). A link to AllGenes assembly via url: http://www.cbil.upenn.edu/servlet/allgenes-dev/servlet?page=rna&id=DT. MusDoTS_BestNRHits_07-31-01.dat.gz contains a DoTS RNA ID followed by the "best hit" to nrdb (protein), the p-value and the length and % identity of the best HSP. Note that only hits with p-values less than 10E-5 are provided. If the DoTS assembly contains an mRNA then the accession for the longest mRNA is given instead. A sample line: DT.55139862: 168|NP_060613.1, pVal=6e-121, ML=248, %=94 DoTS ID: accession preceeded by our internal ID for Refseq proteins, p-value, length of best HSP, % identity of best HSP. Sample line with contained mRNA instead of a protein hit: DT.55136389: 22|AK017668 - contained mRNA DoTS ID: accession preceeded by our internal ID for GenBank (22) - statement that the assembly contains mRNA. Our external database IDs: 3 - nrdb (EMBL) 4 - nrdb (DDBJ) 5 - nrdb (PIR) 22 - GenBank 37 - SWISS-PROT 78 - EMBL 168 - nrdb (RefSeq) 992 - NCBI RefSeq musDoTS_GOFunction.tab.gz contains GO function predictions for musDoTS. The file is tab delimited: For example, the following line represents the GO Function predictions for musDoTS Assembly 480685 (DT.480685): 480685 3824 3978 16853 16854 16857 This implies that the musDoTS assembly 480685 has GO IDs 3824, 3978, 16853, 16854, 16857 predicted. All GO Function predictions provided here are based on the following: 1) Exclusion of all IEA associations in the rule-generation phase 2) Exclusion of all 'Molecular Function Unknown' associations in the rule generation phase 3) Both CDD and ProDom were used for rule generation (learned domain- function associations) ==================================================================== The CBIL Software and Data License, Version 1.0 Copyright (c) 2001 The Computational Biology and Informatics Laboratory (CBIL) at the University of Pennsylvania. All rights reserved. Redistribution and use of software in source and binary forms or of data, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code, binary software or data alone must retain the above copyright notice, this list of conditions and the following disclaimer. 2. 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