[Seqinr-commits] r1592 - pkg/inst/doc/src/appendix
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Apr 23 13:13:42 CEST 2009
Author: lobry
Date: 2009-04-23 13:13:42 +0200 (Thu, 23 Apr 2009)
New Revision: 1592
Modified:
pkg/inst/doc/src/appendix/subsequences.tex
Log:
R 2.9.0
Modified: pkg/inst/doc/src/appendix/subsequences.tex
===================================================================
--- pkg/inst/doc/src/appendix/subsequences.tex 2009-04-23 11:01:09 UTC (rev 1591)
+++ pkg/inst/doc/src/appendix/subsequences.tex 2009-04-23 11:13:42 UTC (rev 1592)
@@ -4,7 +4,7 @@
\title{Informations about databases available at pbil}
\author{Lobry, J.R.}
-\usepackage{/Library/Frameworks/R.framework/Resources/share/texmf/Sweave}
+\usepackage{Sweave}
\begin{document}
%
% To change the R input/output style:
@@ -62,16 +62,17 @@
[5] "ensembl" "refseq" "nrsub" "hobacnucl"
[9] "hobacprot" "hovergendna" "hovergen" "hogenom"
[13] "hogenomdna" "hogennucl" "hogenprot" "hoverclnu"
-[17] "hoverclpr" "homolens" "homolensdna" "greview"
-[21] "polymorphix" "emglib" "HAMAPnucl" "HAMAPprot"
-[25] "hoppsigen" "nurebnucl" "nurebprot" "taxobacgen"
-[29] "emblTP" "swissprotTP" "hoverprotTP" "hovernuclTP"
-[33] "trypano" "ensembl24" "ensembl34" "ensembl41"
-[37] "ensembl47" "ensembl49" "macaca45" "dog45"
-[41] "dog47" "equus49" "pongo49" "rattus49"
-[45] "mouse38" "homolens4" "homolens4dna" "hogendnucl"
-[49] "hogendprot" "genomicro1" "genomicro2" "genomicro3"
-[53] "genomicro4"
+[17] "hoverclpr" "homolens3" "homolens3dna" "homolens"
+[21] "homolensdna" "greview" "polymorphix" "emglib"
+[25] "HAMAPnucl" "HAMAPprot" "taxobacgen" "apis"
+[29] "human" "emblTP" "swissprotTP" "hoverprotTP"
+[33] "hovernuclTP" "trypano" "ensembl24" "ensembl34"
+[37] "ensembl41" "ensembl47" "ensembl49" "macaca45"
+[41] "dog45" "dog47" "equus49" "pongo49"
+[45] "rattus49" "mouse38" "homolens4" "homolens4dna"
+[49] "hoppsigen" "nurebnucl" "nurebprot" "hogendnucl"
+[53] "hogendprot" "genomicro1" "genomicro2" "genomicro3"
+[57] "genomicro4" "dickeya" "tetra53" "trypanosoma"
\end{Soutput}
\end{Schunk}
@@ -130,8 +131,8 @@
\section{ genbank }
\textbf{Bank details}
**** ACNUC Data Base Content **** \\
- GenBank Rel. 167 (15 August 2008) Last Updated: Oct 26, 2008\\
-97,378,213,581 bases; 96,406,734 sequences; 5,646,527 subseqs; 525,953 refers.\\
+ GenBank Rel. 171 (15 April 2009) Last Updated: Apr 23, 2009\\
+103,287,086,629 bases; 103,570,547 sequences; 6,354,023 subseqs; 549,786 refers.\\
Software by M. Gouy, Lab. Biometrie et Biologie Evolutive, Universite Lyon I
\textbf{Type names}
@@ -139,24 +140,24 @@
\hline \hline
name & description & count \\
\hline
-CDS & .PE protein coding region & 6,067,613 \\
-LOCUS & sequenced DNA fragment & 93,511,529 \\
-MISC\_RNA & .RN other structural RNA coding region & 583,588 \\
-RRNA & .RR mature ribosomal RNA & 1,499,635 \\
+CDS & .PE protein coding region & 6,900,945 \\
+LOCUS & sequenced DNA fragment & 100,225,982 \\
+MISC\_RNA & .RN other structural RNA coding region & 643,091 \\
+RRNA & .RR mature ribosomal RNA & 1,722,748 \\
SCRNA & .SC small cytoplasmic RNA & 146 \\
SNRNA & .SN small nuclear RNA & 418 \\
-TMRNA & .TM transfer messenger RNA & 306 \\
-TRNA & .TR mature transfer RNA & 390,026 \\
+TMRNA & .TM transfer messenger RNA & 364 \\
+TRNA & .TR mature transfer RNA & 430,876 \\
\hline
- & Total: & 102,053,261 \\
+ & Total: & 109,924,570 \\
\hline \hline
\end{tabular}
\section{ embl }
\textbf{Bank details}
**** ACNUC Data Base Content **** \\
- EMBL Library Release 96 (September 2008) Last Updated: Oct 25, 2008\\
-118,652,592,128 bases; 99,263,575 sequences; 12,793,590 subseqs; 513,868 refers.\\
+ EMBL Library Release 99 (March 2009) Last Updated: Apr 23, 2009\\
+128,033,198,490 bases; 106,636,474 sequences; 13,957,419 subseqs; 538,628 refers.\\
Software by M. Gouy, Laboratoire de biometrie, Universite Lyon I
\textbf{Type names}
@@ -164,25 +165,25 @@
\hline \hline
name & description & count \\
\hline
-CDS & .PE protein coding region & 13,234,878 \\
-ID & Locus entry & 96,277,087 \\
-MISC\_RNA & .RN other structural RNA coding region & 581,809 \\
-NCRNA & .NC non protein-coding RNA & 58,752 \\
-RRNA & .RR Ribosomal RNA coding gene & 1,500,663 \\
+CDS & .PE protein coding region & 14,501,284 \\
+ID & Locus entry & 103,200,038 \\
+MISC\_RNA & .RN other structural RNA coding region & 641,350 \\
+NCRNA & .NC non protein-coding RNA & 70,447 \\
+RRNA & .RR Ribosomal RNA coding gene & 1,725,176 \\
SCRNA & .SC small cytoplasmic RNA & 0 \\
SNRNA & .SN small nuclear RNA & 0 \\
-TMRNA & .TM transfer messenger RNA & 134 \\
-TRNA & .TR Transfer RNA coding gene & 403,842 \\
+TMRNA & .TM transfer messenger RNA & 206 \\
+TRNA & .TR Transfer RNA coding gene & 455,392 \\
\hline
- & Total: & 112,057,165 \\
+ & Total: & 120,593,893 \\
\hline \hline
\end{tabular}
\section{ emblwgs }
\textbf{Bank details}
**** ACNUC Data Base Content **** \\
- EMBL Whole Genome Shotgun sequences Release 96 (September 2008) \\
-118,606,277,503 bases; 40,248,013 sequences; 1,474,573 subseqs; 523 refers.\\
+ EMBL Whole Genome Shotgun sequences Release 99 (March 2009) \\
+143,979,753,892 bases; 49,058,862 sequences; 1,634,710 subseqs; 637 refers.\\
Retrieval software by M. Gouy, Biometrie et Biologie Evolutive, Univ Lyon I.
\textbf{Type names}
@@ -190,23 +191,23 @@
\hline \hline
name & description & count \\
\hline
-CDS & .PE protein coding region & 1,449,786 \\
-ID & EMBL sequence data library entry & 40,247,551 \\
-MISC\_RNA & .RN other structural RNA coding region & 1,365 \\
-RRNA & .RR ribosomal RNA coding region & 3,253 \\
+CDS & .PE protein coding region & 1,606,862 \\
+ID & EMBL sequence data library entry & 49,058,182 \\
+MISC\_RNA & .RN other structural RNA coding region & 1,323 \\
+RRNA & .RR ribosomal RNA coding region & 3,742 \\
SCRNA & .SC small cytoplasmic RNA coding region & 0 \\
SNRNA & .SN small nuclear RNA coding region & 0 \\
-TRNA & .TR transfer RNA coding region & 20,631 \\
+TRNA & .TR transfer RNA coding region & 23,463 \\
\hline
- & Total: & 41,722,586 \\
+ & Total: & 50,693,572 \\
\hline \hline
\end{tabular}
\section{ swissprot }
\textbf{Bank details}
**** ACNUC Data Base Content **** \\
- UniProt Rel. 14 (SWISS-PROT 56 + TrEMBL 39): Last Updated: Aug 28, 2008\\
- 2,097,290,313 amino acids; 6,462,751 sequences; 297,653 references.\\
+ UniProt Rel. 15 (SWISS-PROT 57 + TrEMBL 40): Last Updated: Apr 21, 2009\\
+ 2,619,864,771 amino acids; 7,990,560 sequences; 309,067 references.\\
Non-redundant compilation of SWISS-PROT + TrEMBL\\
Software by M. Gouy \& L. Duret, Laboratoire de biometrie, Universite Lyon I.
@@ -270,23 +271,26 @@
5'INT & .5I 5'intron & 0 \\
5'NCR & .5F 5'-non coding region & 800,830 \\
CDS & .PE protein coding region & 892,572 \\
+GENE & .GN gene & 805,489 \\
ID & EMBL sequence data library entry & 3,499,715 \\
INT\_INT & .IN internal intron & 7,157,683 \\
MISC\_RNA & .RN other structural RNA coding region & 130,547 \\
+MRNA & .MR mRNA & 892,572 \\
RRNA & .RR ribosomal RNA coding region & 0 \\
SCRNA & .SC small cytoplasmic RNA coding region & 0 \\
SNRNA & .SN small nuclear RNA coding region & 0 \\
TRNA & .TR transfer RNA coding region & 0 \\
\hline
- & Total: & 12,788,788 \\
+ & Total: & 14,486,849 \\
\hline \hline
\end{tabular}
\section{ refseq }
\textbf{Bank details}
- **** ACNUC Data Base Content **** \\
- RefSeq 15.0 (1 January 2006) Last Updated: Jan 23, 2006\\
-1,055,245,496 bases; 625,928 sequences; 254,162 subseqs; 205,831 refers.\\
+ **** ACNUC Data Base Content **** \\
+ RNA sequences - Release 33 (January 16, 2009) Last Updated: Feb 13, 2009\\
+2,746,151,813 bases; 1,685,610 sequences; 522,605 subseqs; 142,084 refers.\\
+ NCBI Reference Sequence (RefSeq) Database\\
Software by M. Gouy \& M. Jacobzone, Laboratoire de biometrie, Universite Lyon I
\textbf{Type names}
@@ -298,16 +302,16 @@
3'NCR & .3F 3'-non coding region & 0 \\
5'INT & .5I 5'intron & 0 \\
5'NCR & .5F 5'-non coding region & 0 \\
-CDS & .PE protein coding region & 624,776 \\
+CDS & .PE protein coding region & 1,641,694 \\
INT\_INT & .IN internal intron & 0 \\
-LOCUS & sequenced DNA fragment & 255,273 \\
-MISC\_RNA & .RN other structural RNA coding region & 8 \\
-RRNA & .RR ribosomal RNA coding region & 0 \\
-SCRNA & .SC small cytoplasmic RNA coding region & 2 \\
-SNRNA & .SN small nuclear RNA coding region & 22 \\
-TRNA & .TR transfer RNA coding region & 9 \\
+LOCUS & sequenced DNA fragment & 564,617 \\
+MISC\_RNA & .RN other structural RNA coding region & 0 \\
+RRNA & .RR ribosomal RNA coding region & 1,904 \\
+SCRNA & .SC small cytoplasmic RNA coding region & 0 \\
+SNRNA & .SN small nuclear RNA coding region & 0 \\
+TRNA & .TR transfer RNA coding region & 0 \\
\hline
- & Total: & 880,090 \\
+ & Total: & 2,208,215 \\
\hline \hline
\end{tabular}
@@ -502,7 +506,7 @@
\textbf{Bank details}
**** ACNUC Data Base Content **** \\
HOGENOM - genomic data - Release 03 (Oct 14 2005) Last Updated: Nov 7, 2005\\
-2,538,433,251 bases; 227,950 sequences; 4,136,134 subseqs; 82,281 refers.\\
+2,538,433,251 bases; 227,950 sequences; 3,166,480 subseqs; 82,283 refers.\\
\\
Fully Sequenced Organisms\\
Protein data from http://www.ebi.ac.uk/proteome/ (August, 2005)\\
@@ -523,20 +527,20 @@
\hline \hline
name & description & count \\
\hline
+3'INT & .3I 3'intron & 340 \\
+3'NCR & .3F 3'-non coding region & 852,742 \\
+5'INT & .5I 5'intron & 1,445 \\
+5'NCR & .5F 5'-non coding region & 873,248 \\
+CDS & .PE protein coding region & 1,064,998 \\
ID & EMBL sequence data library entry & 204,502 \\
-CDS & .PE protein coding region & 1,060,241 \\
-TRNA & .TR transfer RNA coding region & 49,216 \\
-RRNA & .RR ribosomal RNA coding region & 5,813 \\
-MISC\_RNA & .RN other structural RNA coding region & 861 \\
+INT\_INT & .IN internal intron & 646,105 \\
+MISC\_RNA & .RN other structural RNA coding region & 860 \\
+RRNA & .RR ribosomal RNA coding region & 5,819 \\
SCRNA & .SC small cytoplasmic RNA coding region & 29 \\
SNRNA & .SN small nuclear RNA coding region & 459 \\
-3'INT & .3I 3'intron & 309 \\
-3'NCR & .3F 3'-non coding region & 1,247,297 \\
-5'INT & .5I 5'intron & 1,263 \\
-5'NCR & .5F 5'-non coding region & 1,158,238 \\
-INT\_INT & .IN internal intron & 635,856 \\
+TRNA & .TR transfer RNA coding region & 49,239 \\
\hline
- & Total: & 4,364,084 \\
+ & Total: & 3,699,786 \\
\hline \hline
\end{tabular}
@@ -614,6 +618,113 @@
\textbf{Type names}
There are no subsequence type in this database
+\section{ homolens3 }
+\textbf{Bank details}
+ **** ACNUC Data Base Content **** \\
+ HOMOLENS 3 - Homologous genes from Ensembl Last Updated: Jan 19, 2007\\
+ 224,528,520 amino acids; 474,339 sequences; 0 references.\\
+ \\
+ Ensembl 41 Organisms Translated CDS\\
+Aedes aegypti 41\_1a 11360/0/2/0 (0\%/0\%/0\%)\\
+Anopheles gambiae 41\_3d 13510/0/31/0 (0\%/0\%/0\%)\\
+Apis mellifera 38\_2d 27755/1/269/0 (0\%/0\%/0\%)\\
+Bos taurus 41\_2 32556/7/620/12 (0\%/1\%/0\%)\\
+Caenorhabditis elegans 41\_160 25218/1/0/0 (0\%/0\%/0\%)\\
+Canis familiaris 41\_1j 29813/0/0/0 (0\%/0\%/0\%)\\
+Caenorhabditis briggsae 25 14712/0/23/1 (0\%/0\%/0\%)\\
+Ciona intestinalis 41\_2c 20000/0/128/0 (0\%/0\%/0\%)\\
+Ciona savignyi 41\_2b 20150/1/27/0 (0\%/0\%/0\%)\\
+Danio rerio 41\_6b 36065/5/361/0 (0\%/1\%/0\%)\\
+Dasypus novemcinctus 40\_1 13567/12/8857/0 (0\%/65\%/0\%)\\
+Drosophila melanogaster 41\_43 19577/33/1/0 (0\%/0\%/0\%)\\
+Echinops telfairi 40\_1 14309/8/9348/0 (0\%/65\%/0\%)\\
+Gallus gallus 41\_1p 20667/13/455/0 (0\%/2\%/0\%)\\
+Gasterosteus aculeatus 41\_1a 27181/13/138/0 (0\%/0\%/0\%)\\
+Homo sapiens 41\_36c 47004/41/6/0 (0\%/0\%/0\%)\\
+Loxodonta africana 40\_1 14366/10/9618/0 (0\%/66\%/0\%)\\
+Macaca mulatta 41\_10a 36446/14/491/0 (0\%/1\%/0\%)\\
+Monodelphis domestica 41\_3a 30358/0/80/0 (0\%/0\%/0\%)\\
+Mus musculus 41\_36b 29026/34/2/0 (0\%/0\%/0\%)\\
+Oryctolagus cuniculus 41\_1a 13705/4/8615/0 (0\%/62\%/0\%)\\
+Oryzias latipes 41\_1 25880/0/546/0 (0\%/2\%/0\%)\\
+Pan troglodytes 41\_21 32667/4/739/0 (0\%/2\%/0\%)\\
+Rattus norvegicus 41\_34k 32996/34/686/0 (0\%/2\%/0\%)\\
+Saccharomyces cerevisiae 41\_1d 4767/2/0/0 (0\%/0\%/0\%)\\
+Takifugu rubripes 41\_4c 22102/0/283/0 (0\%/1\%/0\%)\\
+Tetraodon nigroviridis 41\_1g 15841/1/225/0 (0\%/1\%/0\%)\\
+Xenopus tropicalis 41\_41b 28324/0/626/0 (0\%/2\%/0\%)\\
+ \\
+ \\
+Software: M. Gouy \& M. Jacobzone\\
+Data maintenance: L. Duret \& S. Penel\\
+\\
+Laboratoire de Biometrie et Biologie Evolutive\\
+UMR CNRS 5558, Universite Claude Bernard - Lyon 1 \\
+43, bd du 11 Novembre 1918 F-69622 Villeurbanne Cedex\\
+
+
+\textbf{Type names}
+There are no subsequence type in this database
+\section{ homolens3dna }
+\textbf{Bank details}
+ **** ACNUC Data Base Content **** \\
+ HOMOLENS 3 Homologous genes from Ensembl 41 Last Updated: Jan 19, 2007\\
+32,635,729,329 bases; 81,903 sequences; 5,717,782 subseqs; 0 refers.\\
+\\
+Aedes aegypti 41\_1a 11360/0/2/0 (0\%/0\%/0\%)\\
+Anopheles gambiae 41\_3d 13510/0/31/0 (0\%/0\%/0\%)\\
+Apis mellifera 38\_2d 27755/1/269/0 (0\%/0\%/0\%)\\
+Bos taurus 41\_2 32556/7/620/12 (0\%/1\%/0\%)\\
+Caenorhabditis elegans 41\_160 25218/1/0/0 (0\%/0\%/0\%)\\
+Canis familiaris 41\_1j 29813/0/0/0 (0\%/0\%/0\%)\\
+Caenorhabditis briggsae 25 14712/0/23/1 (0\%/0\%/0\%)\\
+Ciona intestinalis 41\_2c 20000/0/128/0 (0\%/0\%/0\%)\\
+Ciona savignyi 41\_2b 20150/1/27/0 (0\%/0\%/0\%)\\
+Danio rerio 41\_6b 36065/5/361/0 (0\%/1\%/0\%)\\
+Dasypus novemcinctus 40\_1 13567/12/8857/0 (0\%/65\%/0\%)\\
+Drosophila melanogaster 41\_43 19577/33/1/0 (0\%/0\%/0\%)\\
+Echinops telfairi 40\_1 14309/8/9348/0 (0\%/65\%/0\%)\\
+Gallus gallus 41\_1p 20667/13/455/0 (0\%/2\%/0\%)\\
+Gasterosteus aculeatus 41\_1a 27181/13/138/0 (0\%/0\%/0\%)\\
+Homo sapiens 41\_36c 47004/41/6/0 (0\%/0\%/0\%)\\
+Loxodonta africana 40\_1 14366/10/9618/0 (0\%/66\%/0\%)\\
+Macaca mulatta 41\_10a 36446/14/491/0 (0\%/1\%/0\%)\\
+Monodelphis domestica 41\_3a 30358/0/80/0 (0\%/0\%/0\%)\\
+Mus musculus 41\_36b 29026/34/2/0 (0\%/0\%/0\%)\\
+Oryctolagus cuniculus 41\_1a 13705/4/8615/0 (0\%/62\%/0\%)\\
+Oryzias latipes 41\_1 25880/0/546/0 (0\%/2\%/0\%)\\
+Pan troglodytes 41\_21 32667/4/739/0 (0\%/2\%/0\%)\\
+Rattus norvegicus 41\_34k 32996/34/686/0 (0\%/2\%/0\%)\\
+Saccharomyces cerevisiae 41\_1d 4767/2/0/0 (0\%/0\%/0\%)\\
+Takifugu rubripes 41\_4c 22102/0/283/0 (0\%/1\%/0\%)\\
+Tetraodon nigroviridis 41\_1g 15841/1/225/0 (0\%/1\%/0\%)\\
+Xenopus tropicalis 41\_41b 28324/0/626/0 (0\%/2\%/0\%)\\
+\\
+ \\
+Software by M. Gouy \& M. Jacobzone, Laboratoire de biometrie, Universite Lyon I
+
+\textbf{Type names}
+\noindent\begin{tabular}{llr}
+\hline \hline
+name & description & count \\
+\hline
+3'INT & .3I 3'intron & 0 \\
+3'NCR & .3F 3'-non coding region & 188,371 \\
+5'INT & .5I 5'intron & 0 \\
+5'NCR & .5F 5'-non coding region & 485,692 \\
+CDS & .PE protein coding region & 659,680 \\
+ID & EMBL sequence data library entry & 81,903 \\
+INT\_INT & .IN internal intron & 4,339,670 \\
+MISC\_RNA & .RN other structural RNA coding region & 44,369 \\
+RRNA & .RR ribosomal RNA coding region & 0 \\
+SCRNA & .SC small cytoplasmic RNA coding region & 0 \\
+SNRNA & .SN small nuclear RNA coding region & 0 \\
+TRNA & .TR transfer RNA coding region & 0 \\
+\hline
+ & Total: & 5,799,685 \\
+\hline \hline
+\end{tabular}
+
\section{ homolens }
\textbf{Bank details}
**** ACNUC Data Base Content ****\\
@@ -822,105 +933,108 @@
There was a problem while trying to open this bank.
\section{ HAMAPprot }
There was a problem while trying to open this bank.
-\section{ hoppsigen }
+\section{ taxobacgen }
\textbf{Bank details}
-NA
+ **** ACNUC Data Base Content ****\\
+ TaxoBacGen Rel. 7 (September 2005)\\
+1,151,149,763 bases; 254,335 sequences; 847,767 subseqs; 63,879 refers.\\
+ Data compiled from GenBank by Gregory Devulder \\
+ Laboratoire de Biometrie \& Biologie Evolutive, Univ Lyon I\\
+------------------------------\\
+This database is a taxonomic genomic database. \\
+It results from an expertise crossing the data nomenclature database DSMZ\\
+\[http://www.dsmz.de/species/bacteria.htm Deutsche Sammlung von\\
+Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany\]\\
+and GenBank. \\
+- Only contains sequences described under species present in \\
+Bacterial Nomenclature Up-to-date.\\
+- Names of species and genus validly published according to the\\
+Bacteriological Code (names with standing in nomenclature) is \\
+added in field "DEFINITION".\\
+- A keyword "type strain" is added in field "FEATURES/source/strain" in\\
+GenBank format definition to easyly identify Type Strain.\\
+Taxobacgen is a genomic database designed for studies based on a strict\\
+respect of up-to-date nomenclature and taxonomy.
\textbf{Type names}
\noindent\begin{tabular}{llr}
\hline \hline
name & description & count \\
\hline
-ID & EMBL sequence data library entry & 9,757 \\
-CDS & .PE protein coding region & 3,814 \\
-TRNA & .TR transfer RNA coding region & 0 \\
-RRNA & .RR ribosomal RNA coding region & 0 \\
-MISC\_RNA & .RN other structural RNA coding region & 0 \\
-SCRNA & .SC small cytoplasmic RNA coding region & 0 \\
+CDS & .PE protein coding region & 879,340 \\
+LOCUS & sequenced DNA fragment & 168,243 \\
+MISC\_RNA & .RN other structural RNA coding region & 3,720 \\
+RRNA & .RR ribosomal RNA coding region & 34,965 \\
+SCRNA & .SC small cytoplasmic RNA coding region & 36 \\
SNRNA & .SN small nuclear RNA coding region & 0 \\
-CDE & .PS & 9,757 \\
-PPGENE & .PP & 9,757 \\
-3'FL & .3F & 3,656 \\
-5'FL & .5F & 730 \\
-DIRECT\_REPEAT & .DR & 15,592 \\
-REPEAT\_REGION & .RR & 133,215 \\
-POLYA\_REGION & .PA & 1,694 \\
-FL\_REPEAT & .FR & 0 \\
+TRNA & .TR transfer RNA coding region & 15,798 \\
\hline
- & Total: & 187,972 \\
+ & Total: & 1,102,102 \\
\hline \hline
\end{tabular}
-\section{ nurebnucl }
+\section{ apis }
\textbf{Bank details}
- **** ACNUC Data Base Content **** \\
- Nurebase 4.0 (26 September 2003) Last Updated: NOV 27, 2003\\
-2,356,663 bases; 664 sequences; 518 subseqs; 787 refers.\\
-Software by M. Gouy \& M. Jacobzone, Laboratoire de biometrie, Universite Lyon I
+ **** ACNUC Data Base Content **** \\
+ Apis mellifera - based on Amel\_4.0 (March,2006) Last Updated: Feb 25, 2009\\
+ 217,194,876 bases; 16 sequences; 60,592 subseqs; 0 refers.\\
+ Retrieval software by M. Gouy \& M. Jacobzone, Lab. de Biometrie, UCB Lyon.\\
+ Data maintenance: L. Duret \& S. Penel\\
+\\
+ Laboratoire de Biometrie et Biologie Evolutive\\
+ UMR CNRS 5558, Universite Claude Bernard - Lyon 1 \\
+ 43, bd du 11 Novembre 1918 F-69622 Villeurbanne Cedex\\
+
\textbf{Type names}
\noindent\begin{tabular}{llr}
\hline \hline
name & description & count \\
\hline
-CDS & .PE protein coding region & 767 \\
-ID & EMBL sequence data library entry & 415 \\
+3'INT & .3I 3'intron & 0 \\
+3'NCR & .3F 3'-non coding region & 6,545 \\
+5'INT & .5I 5'intron & 0 \\
+5'NCR & .5F 5'-non coding region & 6,543 \\
+CDS & .PE protein coding region & 6,704 \\
+ID & EMBL sequence data library entry & 16 \\
+INT\_INT & .IN internal intron & 40,800 \\
MISC\_RNA & .RN other structural RNA coding region & 0 \\
RRNA & .RR ribosomal RNA coding region & 0 \\
SCRNA & .SC small cytoplasmic RNA coding region & 0 \\
SNRNA & .SN small nuclear RNA coding region & 0 \\
TRNA & .TR transfer RNA coding region & 0 \\
\hline
- & Total: & 1,182 \\
+ & Total: & 60,608 \\
\hline \hline
\end{tabular}
-\section{ nurebprot }
+\section{ human }
\textbf{Bank details}
**** ACNUC Data Base Content **** \\
- Nurebase 4.0 (26 September 2003) Last Updated: NOV 27, 2003\\
- 277,024 amino acids; 525 sequences; 634 references.\\
-Software by M. Gouy \& M. Jacobzone, Laboratoire de biometrie, Universite Lyon I
+Homo sapiens - Release Ensembl Release 52 Databases. - (03/03/09) Last Updated: Mar 3, 2009\\
+3,664,692,642 bases; 3,860 sequences; 676,152 subseqs; 0 refers.\\
+MENU Nber of lines= 21
\textbf{Type names}
-There are no subsequence type in this database
-\section{ taxobacgen }
-\textbf{Bank details}
- **** ACNUC Data Base Content ****\\
- TaxoBacGen Rel. 7 (September 2005)\\
-1,151,149,763 bases; 254,335 sequences; 847,767 subseqs; 63,879 refers.\\
- Data compiled from GenBank by Gregory Devulder \\
- Laboratoire de Biometrie \& Biologie Evolutive, Univ Lyon I\\
-------------------------------\\
-This database is a taxonomic genomic database. \\
-It results from an expertise crossing the data nomenclature database DSMZ\\
-\[http://www.dsmz.de/species/bacteria.htm Deutsche Sammlung von\\
-Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany\]\\
-and GenBank. \\
-- Only contains sequences described under species present in \\
-Bacterial Nomenclature Up-to-date.\\
-- Names of species and genus validly published according to the\\
-Bacteriological Code (names with standing in nomenclature) is \\
-added in field "DEFINITION".\\
-- A keyword "type strain" is added in field "FEATURES/source/strain" in\\
-GenBank format definition to easyly identify Type Strain.\\
-Taxobacgen is a genomic database designed for studies based on a strict\\
-respect of up-to-date nomenclature and taxonomy.
-
-\textbf{Type names}
\noindent\begin{tabular}{llr}
\hline \hline
name & description & count \\
\hline
-CDS & .PE protein coding region & 879,340 \\
-LOCUS & sequenced DNA fragment & 168,243 \\
-MISC\_RNA & .RN other structural RNA coding region & 3,720 \\
-RRNA & .RR ribosomal RNA coding region & 34,965 \\
-SCRNA & .SC small cytoplasmic RNA coding region & 36 \\
+3'INT & .3I 3'intron & 0 \\
+3'NCR & .3F 3'-non coding region & 23,783 \\
+5'INT & .5I 5'intron & 0 \\
+5'NCR & .5F 5'-non coding region & 46,304 \\
+CDS & .PE protein coding region & 55,115 \\
+ID & EMBL sequence data library entry & 3,860 \\
+INT\_INT & .IN internal intron & 476,982 \\
+MISC\_RNA & .RN other structural RNA coding region & 18,853 \\
+MRNA & .MR mRNA & 55,115 \\
+RRNA & .RR ribosomal RNA coding region & 0 \\
+SCRNA & .SC small cytoplasmic RNA coding region & 0 \\
SNRNA & .SN small nuclear RNA coding region & 0 \\
-TRNA & .TR transfer RNA coding region & 15,798 \\
+TRNA & .TR transfer RNA coding region & 0 \\
\hline
- & Total: & 1,102,102 \\
+ & Total: & 680,012 \\
\hline \hline
\end{tabular}
@@ -1307,15 +1421,17 @@
5'INT & .5I 5'intron & 0 \\
5'NCR & .5F 5'-non coding region & 800,830 \\
CDS & .PE protein coding region & 892,572 \\
+GENE & .GN gene & 805,489 \\
ID & EMBL sequence data library entry & 3,499,715 \\
INT\_INT & .IN internal intron & 7,157,683 \\
MISC\_RNA & .RN other structural RNA coding region & 130,547 \\
+MRNA & .MR mRNA & 892,572 \\
RRNA & .RR ribosomal RNA coding region & 0 \\
SCRNA & .SC small cytoplasmic RNA coding region & 0 \\
SNRNA & .SN small nuclear RNA coding region & 0 \\
TRNA & .TR transfer RNA coding region & 0 \\
\hline
- & Total: & 12,788,788 \\
+ & Total: & 14,486,849 \\
\hline \hline
\end{tabular}
@@ -1641,6 +1757,68 @@
\hline \hline
\end{tabular}
+\section{ hoppsigen }
+\textbf{Bank details}
+NA
+
+\textbf{Type names}
+\noindent\begin{tabular}{llr}
+\hline \hline
+name & description & count \\
+\hline
+ID & EMBL sequence data library entry & 9,757 \\
+CDS & .PE protein coding region & 3,814 \\
+TRNA & .TR transfer RNA coding region & 0 \\
+RRNA & .RR ribosomal RNA coding region & 0 \\
+MISC\_RNA & .RN other structural RNA coding region & 0 \\
+SCRNA & .SC small cytoplasmic RNA coding region & 0 \\
+SNRNA & .SN small nuclear RNA coding region & 0 \\
+CDE & .PS & 9,757 \\
+PPGENE & .PP & 9,757 \\
+3'FL & .3F & 3,656 \\
+5'FL & .5F & 730 \\
+DIRECT\_REPEAT & .DR & 15,592 \\
+REPEAT\_REGION & .RR & 133,215 \\
+POLYA\_REGION & .PA & 1,694 \\
+FL\_REPEAT & .FR & 0 \\
+\hline
+ & Total: & 187,972 \\
+\hline \hline
+\end{tabular}
+
+\section{ nurebnucl }
+\textbf{Bank details}
+ **** ACNUC Data Base Content **** \\
+ Nurebase 4.0 (26 September 2003) Last Updated: NOV 27, 2003\\
+2,356,663 bases; 664 sequences; 518 subseqs; 787 refers.\\
+Software by M. Gouy \& M. Jacobzone, Laboratoire de biometrie, Universite Lyon I
+
+\textbf{Type names}
+\noindent\begin{tabular}{llr}
+\hline \hline
+name & description & count \\
+\hline
+CDS & .PE protein coding region & 767 \\
+ID & EMBL sequence data library entry & 415 \\
+MISC\_RNA & .RN other structural RNA coding region & 0 \\
+RRNA & .RR ribosomal RNA coding region & 0 \\
+SCRNA & .SC small cytoplasmic RNA coding region & 0 \\
+SNRNA & .SN small nuclear RNA coding region & 0 \\
+TRNA & .TR transfer RNA coding region & 0 \\
+\hline
+ & Total: & 1,182 \\
+\hline \hline
+\end{tabular}
+
+\section{ nurebprot }
+\textbf{Bank details}
+ **** ACNUC Data Base Content **** \\
+ Nurebase 4.0 (26 September 2003) Last Updated: NOV 27, 2003\\
+ 277,024 amino acids; 525 sequences; 634 references.\\
+Software by M. Gouy \& M. Jacobzone, Laboratoire de biometrie, Universite Lyon I
+
+\textbf{Type names}
+There are no subsequence type in this database
\section{ hogendnucl }
\textbf{Bank details}
**** ACNUC Data Base Content **** \\
@@ -1825,31 +2003,123 @@
\hline
& Total: & 54,529 \\
\hline \hline
+\end{tabular}
+
+\section{ dickeya }
+\textbf{Bank details}
+ **** ACNUC Data Base Content **** \\
+ Dickeya dadantii 3937 Chromosome(Geb 2, 2009) Last Updated: Feb 2, 2009\\
+4,922,802 bases; 1 sequences; 4,725 subseqs; 0 refers.\\
+Software by M. Gouy, Lab. Biometrie et Biologie Evolutive, Universite Lyon I
+
+\textbf{Type names}
+\noindent\begin{tabular}{llr}
+\hline \hline
+name & description & count \\
+\hline
+3'INT & .3I 3'intron & 0 \\
+3'NCR & .3F 3'-non coding region & 0 \\
+5'INT & .5I 5'intron & 0 \\
+5'NCR & .5F 5'-non coding region & 0 \\
+CDS & .PE protein coding region & 4,609 \\
+INT\_INT & .IN internal intron & 0 \\
+LOCUS & sequenced DNA fragment & 1 \\
+MISC\_RNA & .RN other structural RNA coding region & 19 \\
+RRNA & .RR ribosomal RNA coding region & 22 \\
+SCRNA & .SC small cytoplasmic RNA coding region & 0 \\
+SNRNA & .SN small nuclear RNA coding region & 0 \\
+TRNA & .TR transfer RNA coding region & 75 \\
+\hline
+ & Total: & 4,726 \\
+\hline \hline
+\end{tabular}
+
+\section{ tetra53 }
+\textbf{Bank details}
+ **** ACNUC Data Base Content **** \\
+ Tetraodon negroviritis - Release 53 - (03/06/09) Last Updated: Mar 6, 2009\\
+358,618,246 bases; 375 sequences; 316,244 subseqs; 0 refers.\\
+MENU Nber of lines= 21
+
+\textbf{Type names}
+\noindent\begin{tabular}{llr}
+\hline \hline
+name & description & count \\
+\hline
+3'INT & .3I 3'intron & 0 \\
+3'NCR & .3F 3'-non coding region & 6,974 \\
+5'INT & .5I 5'intron & 0 \\
+5'NCR & .5F 5'-non coding region & 21,769 \\
+CDS & .PE protein coding region & 23,118 \\
+ID & EMBL sequence data library entry & 375 \\
+INT\_INT & .IN internal intron & 240,437 \\
+MISC\_RNA & .RN other structural RNA coding region & 828 \\
+MRNA & .MR mRNA & 23,118 \\
+RRNA & .RR ribosomal RNA coding region & 0 \\
+SCRNA & .SC small cytoplasmic RNA coding region & 0 \\
+SNRNA & .SN small nuclear RNA coding region & 0 \\
+TRNA & .TR transfer RNA coding region & 0 \\
+\hline
+ & Total: & 316,619 \\
+\hline \hline
+\end{tabular}
+
+\section{ trypanosoma }
+\textbf{Bank details}
+ **** ACNUC Data Base Content **** \\
+Trypanosoma brucei - Chromosome 11 missing (Mar 30, 2009) Last Updated: Apr 3, 2009\\
+20,527,385 bases; 10 sequences; 7,247 subseqs; 4 refers.\\
+Software by M. Gouy, Lab. Biometrie et Biologie Evolutive, Universite Lyon I
+
+\textbf{Type names}
+\noindent\begin{tabular}{llr}
+\hline \hline
+name & description & count \\
+\hline
+3'INT & .3I 3'intron & 0 \\
+3'NCR & .3F 3'-non coding region & 0 \\
+5'INT & .5I 5'intron & 0 \\
+5'NCR & .5F 5'-non coding region & 0 \\
+CDS & .PE protein coding region & 7,089 \\
+ID & EMBL sequence data library entry & 10 \\
+INT\_INT & .IN internal intron & 0 \\
+MISC\_RNA & .RN other structural RNA coding region & 28 \\
+RRNA & .RR ribosomal RNA coding region & 62 \\
+SCRNA & .SC small cytoplasmic RNA coding region & 0 \\
+SNRNA & .SN small nuclear RNA coding region & 5 \\
+TRNA & .TR transfer RNA coding region & 63 \\
+\hline
+ & Total: & 7,257 \\
+\hline \hline
\end{tabular}\end{Schunk}
\section*{Session Informations}
+\begin{scriptsize}
+
This part was compiled under the following \Rlogo{}~environment:
\begin{itemize}
- \item R version 2.8.0 (2008-10-20), \verb|i386-apple-darwin8.8.2|
- \item Locale: \verb|C|
- \item Base packages: base, datasets, grDevices, graphics, methods,
- stats, utils
- \item Other packages: MASS~7.2-44, ade4~1.4-9, ape~2.2-2,
- nlme~3.1-89, quadprog~1.4-11, seqinr~2.0-0, tseries~0.10-16,
- xtable~1.5-4, zoo~1.5-4
- \item Loaded via a namespace (and not attached): grid~2.8.0,
- lattice~0.17-15
+ \item R version 2.9.0 (2009-04-17), \verb|i386-apple-darwin8.11.1|
+ \item Locale: \verb|fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/C/C|
+ \item Base packages: base, datasets, graphics, grDevices, grid,
+ methods, stats, utils
+ \item Other packages: ade4~1.4-11, ape~2.3, grImport~0.4-3,
+ MASS~7.2-46, quadprog~1.4-11, seqinr~2.0-3, tseries~0.10-18,
+ XML~2.3-0, xtable~1.5-5, zoo~1.5-5
+ \item Loaded via a namespace (and not attached): gee~4.13-13,
+ lattice~0.17-22, nlme~3.1-90
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Sun Oct 26 19:31:10 2008
+ \item \Rlogo{} compilation time was: Thu Apr 23 13:09:25 2009
\item \LaTeX{} compilation time was: \today
\end{itemize}
+\end{scriptsize}
+
% END - DO NOT REMOVE THIS LINE
%%%%%%%%%%%% BIBLIOGRAPHY %%%%%%%%%%%%%%%%%
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