Newsgroup: it.comp.os.linux.software
Titolo: [OT] software di analisi proteiche

Salve, immagino di essere OT, ma io sto disperatamente cercando un software
opensource per fare analisi di sequenze proteiche o di acidi nucleici,
simile a winclone o Omiga per windows.
Qualcuno ne conosce?
Grazie!


prova a dare un'occhiata a SAL ( Scient. Application for Linux)
se c'e` qualcosa e` riportato senz'altro li`.
http://chpc06.ch.unito.it/linux/Z/2/
ciao, andrea


OT non sei, se questi siano simili o meno ai programmi per Windows che
citi non so, comunque, ecco qualcosa dal database di debian (con il
ridondande o l'inutile eliminato).  HTH
$ apt-cache search protein
blast2 - Basic Local Alignment Search Tool
garlic - [Chemistry] a free molecular visualization program
garlic-doc - [Chemistry] a molecular visualization program - documents
hmmer - models protein or nucleic acid sequences.
rasmol - molecule visualization and rendering
readseq - [Biology] Conversion between sequence formats
clustalw - [Biology] A multiple sequence alignment program
$ apt-cache search --full protein
Package: blast2
Installed-Size: 906
Version: 6.1.20010709-5
Depends: libc6 (>= 2.2.4-2), ncbi-tools6 (>= 6.1.20010709-1)
Suggests: ncbi-tools-bin, ncbi-tools-x11, vibrant6
Description: Basic Local Alignment Search Tool
 The famous sequence alignment program. This is "official" NCBI version,
 #2. The blastall executable allows you to give a nucleotide or protein
 sequence to the program. It is compared against databases and a summary of
 matches is returned to the user.
 .
 Note that databases are not included in Debian; they must be retrieved
 manually.
Package: garlic
Installed-Size: 532
Version: 1.1-2
Depends: libc6 (>= 2.2.2-2), xlibs (>= 4.0.1-11)
Description: [Chemistry] a free molecular visualization program
 Garlic is probably the most portable molecular visualization program
 in the Unix world. It's written for the investigation of membrane
 proteins. It may be used to visualize other proteins, as well as some
 geometric objects. The name should has something to do with the
 structure and operation of this program. This version of garlic
 recognizes PDB format version 2.1. Garlic may also be used to analyze
 protein sequences.
 .
 Features include (but not limited to):
  o The slab position and thickness are visible in a small window.
  o Atomic bonds as well as atoms are treated as independent drawable
    objects.
  o The atomic and bond colors depend on position. Five mapping modes
    are available (as for slab).
  o Capable to display stereo image.
  o Capable to display other geometric objects, like membrane.
  o Atomic information is available for atom covered by the mouse
    pointer. No click required, just move the mouse pointer over the
    structure!
  o Capable to load more than one structure.
  o Capable to draw Ramachandran plot, helical wheel, Venn diagram,
    averaged hydrophobicity and hydrophobic moment plot.
  o The command prompt is available at the bottom of the main window.
    It is able to display one error message and one command string.
 .
 Author:
  Damir Zucic (
zu...@pref.etfos.hr
), University of Osijek, Croatia.
 .
 Keywords:
  molecular visualization, protein structure, DNA structure, PDB,
  molecular rendering, biological macromolecule
Package: hmmer
Installed-Size: 6852
Version: 2.1.4
Depends: libc6 (>= 2.2.1-2)
Description: models protein or nucleic acid sequences.
 Hmmer is a suite of programs which use profile
 hidden Markov models (profile HMMs) to model
 the primary structure consensus of a family of
 protein or nucleic acid sequences.
 Homepage:  
http://hmmer.wustl.edu/
Package: rasmol
Installed-Size: 1660
Version: 2.6b2-6
Depends: libc6 (>= 2.2.3-1), xlibs (>> 4.0.3)
Description: molecule visualization and rendering
 RasMol is a molecular graphics program intended for the
 visualisation of proteins, nucleic acids and small
 molecules. The program is aimed at display, teaching
 and generation of publication quality images.
 .
 Currently supported input file formats include
 Brookhaven Protein Databank (PDB), Tripos' Alchemy
 and Sybyl Mol2 formats, Molecular Design Limited's
 (MDL) Mol file format, Minnesota Supercomputer
 Center's (MSC) XMol XYZ format and CHARMm format files.
 .
 The loaded molecule may be shown as wireframe, cylinder
 (drieding) stick bonds, alpha-carbon trace, spacefilling
 (CPK) spheres, macromolecular ribbons (either smooth
 shaded solid ribbons or parallel strands),
 hydrogen bonding and dot surface.
 Rasmol homepage: 
http://klaatu.oit.umass.edu:80/microbio/rasmol/
Task: science
Package: readseq
Installed-Size: 168
Version: 1-2
Depends: libc6 (>= 2.2.4-4), ncbi-tools6 (>= 6.1.20010709-1)
Description: [Biology] Conversion between sequence formats
 Reads and writes nucleic/protein sequences in various
 formats. Data files may have multiple sequences.
 Readseq is particularly useful as it automatically detects many
 sequence formats, and interconverts among them.
 .
 URL: 
ftp://ftp.bio.indiana.edu/molbio/readseq/version1
Package: clustalw
Installed-Size: 271
Version: 1.7-8
Depends: libc6 (>= 2.2.2-2)
Description: [Biology] A multiple sequence alignment program
 This interactive console program allows simultaneous alignment
 of many nucleotide or amino acid sequences. It recognizes which
 format is being used and whether the sequences are nucleic acid
 (DNA/RNA) or amino acid (proteins). It outputs alignments in
 various formats such as the Phylip one.

 > simile a winclone o Omiga per windows.
$ apt-cache search protein
blast2 - Basic Local Alignment Search Tool
garlic - [Chemistry] a free molecular visualization program
garlic-doc - [Chemistry] a molecular visualization program - documents
hmmer - models protein or nucleic acid sequences.
rasmol - molecule visualization and rendering
readseq - [Biology] Conversion between sequence formats
clustalw - [Biology] A multiple sequence alignment program
oppure SAL
-- 
Pa.Ped, Como
http://www.fastflow.it/~paolop
VOTE AGAINST SPAM! 
http://www.politik-digital.de/spam/it/
Contro i brevetti software: 
http://petition.eurolinux.org/index_html