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Contents 1 Journals 2 Databases 2.1 Sequences 2.2 Structures 2.3 Literature 2.4 Taxonomy 3 SRS 4 Scripts 5 Alignment 6 Orthology 7 Phylogeny 8 Blast 9 Distant homology 10 Protein analyses 11 Protein Structure Analyses 12 Structural classification 13 Structure-based alignments 14 Structure viewers 15 Grids 16 SVN 17 Linux 17.1 Fedora 17.2 Video/Display 17.3 SSH 17.4 Kernel 17.5 RPM 17.6 Vi 17.7 DVD burning 17.8 Java

Journals

Bioinformatics, BMC Bioinformatics, In Silico Biology, Genome Biology, Applied Bioinformatics

Databases

Sequences

INSDC , DBBJ , EMBL , GenBank , PIR , UniProt

Structures

PDBSum , PDB ,

Literature

PubMed , HubMed

Taxonomy

NCBI-Taxonomy, The Genetic Codes

SRS

DDBJ , Sprot , EBI

Scripts

Phage analysis

Alignment

Muscle, Lobster, Malign, ClustalW, DbClustal, T-coffee [code] [server], FAST [server/code], MultiProt [server/code], Mammooth [server] [code], SAlign [server], K2SA [server], CE-MC [server], DaliLite [server], Protein3dFit [server], MAPS [server] [code], TM-Align [server/code] , OxBench [code], STAMP [code], Comparer [server] , Acana [code] , Chaos [code] , DiAlign [server] [code] , Chaos-DiAlign [server] , Lagan [code] , Vista/Avid [code] , ZPicture [server] , BlastZ [code] , Quasar [code] , ScanMot [server]

Orthology

COG - NCBI, TOGA - TIGR, OrthoMCL DB, OrthoDisease, InParanoid, OrthoStrapper, HOPS, RIO

Phylogeny

POY, Phylip, ProfDist, MrBayes, Ancescon, MrModelTest ,

Blast

NCBI [server] [code] , ParasitesGenome-EBI [server] , DDBJ [server] , ExPASy [server] , WormBase [server] , FlyBase [server] , TcruziDB [server] , GeneDB [server] , EnsEMBL [server] , TcruziDB [server] , ApiDB [server] , UniProt [server] , PIR [server] , NPSA [server] , Yeast [server] ,

Distant homology

Fugue [server], SAM-T02 [server], Gene3D , HHpred [server] , HHsearch [code] , Hmmer [code] ,

Protein analyses

ProDom , Sprot , PFam , AnDom , CDD , Blocks , Systers , NPSA , InterPro , ProTeus ,

Protein Structure Analyses

Modeller , PredictProtein , Sable , SDSC1 , Swiss-Model , CPHmodels , JOY , Astral , SSM , PINTS , PALI , SUPFAM , Dali , Dali Fold Classification , CAFASP4 [server] , LiveBench [server] , EVA [server] ,

Structural classification

SCOP , CATH ,

Structure-based alignments

S4 , Homstrad , DBali , BaliBASE2 , Campass , SCOP:Structural-Alignments , Staccato , SAD ,

Structure viewers

Chimera , Chime , Swiss-PDBviewer , Rasmol , Mice , CosmoPlayer ,

Grids

BioGrid, BITS, Asia Pacific Bio-Grid Initiative, MyGrid, EasyGrid, OurGrid, OpenPBS, OpenMPI, Globus

SVN

Subversion, CVS to SVN Crossover Guide, Subversion (a free book), Subversion Quick Reference (PostScript), Moving a SVN repo, SVN clients

Linux

Fedora

Fedora, Fedora Project, Unofficial Fedora FAQ, Basics, Fedora Legacy, Fedora Docs, Fedora News, Personal Fedora Core 4 Installation Guide,

Video/Display

nVIDIA and FC5, DRI, Livna ATi & RPMs, Proprietary video drivers, ATI proprietary Linux x86 display driver, ATI Radeon X300SE (128MB) PCIe Graphics Card,Is there a driver for ATI Radeon X300 SE ???

SSH

Howto setup SSH keys between machines,

Kernel

Building From src.rpm Files -- Modifying Freetype, Kernel Build, Como compilar kernel 2.6.* no Red Hat 9.0 rápido e fácil, Recompilar Kernel, The Linux Kernel Archives, HowTo Upgrade To The 2.6 Kernel, Fedora Core 4 Kernel Compile Notes

RPM

All you have to know about RPM, RPMforge.net, RPMfind.net, RPM Pbone, FreshRPMs, RPMPan

Vi

Vi Basic Commands

DVD burning

Burning DVD-RW in Linux, Blu-ray Disc/DVD+RW/+R/-R(W) for Linux, CD-Rs and CD-RWs

Java

Custom Java