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T_Coffee is a multiple sequence alignment package. The version included with this distribution of Rocks is v3.84
T-coffee is used for standard alignments and alignment combinations. It is installed at /opt/Bio/t_coffee/ on the Rocks distribution. To use T-Coffee, just type t_coffee at the command line for a list of all possible parameters that can be used. T-coffee recognizes formats such as fasta, clustalw, blast, etc. Example input files are available at /opt/Bio/t_coffee/example/
A simple sequence alignment example is shown below about. It is run against a sample fasta file present in the example directory. Parts of the output are deleted for the sake of brevity. Where missing, output is substituted by ellipses (.....)
[nostromo@rocks-168 ~]$ t_coffee /opt/Bio/t_coffee/example/sample_aln2.fasta
PROGRAM: T-COFFEE (Version_3.84)
-full_log S [0]
-run_name S [0]
-mem_mode S [0] mem
-extend D [1] 1
-extend_mode S [0] very_fast_triplet
-max_n_pair D [0] 10
-seq_name_for_quadruplet S [0] all
-compact S [0] default
-clean S [0] no
-do_self FL [0] 0
-do_normalise D [0] 1000
-template_file S [0]
-in S [0] Mlalign_id_pair Mslow_pair
-seq S [1] /opt/Bio/t_coffee/example/sample_aln2.fasta
-aln S [0]
-method S [0]
.........
-dpa_keep_tmpfile FL [0] 0
-dpa_debug D [0] 0
-multi_thread S [0]
-lib_list S [0]
INPUT FILES
Input File (M) lalign_id_pair
Input File (M) slow_pair
Input File (S) /opt/Bio/t_coffee/example/sample_aln2.fasta Format
clustal_aln
INPUT SEQUENCES: 6 SEQUENCES [PROTEIN]
Input File /opt/Bio/t_coffee/example/sample_aln2.fasta Seq 1cms Length
175 type PROTEIN Struct Unchecked
Input File /opt/Bio/t_coffee/example/sample_aln2.fasta Seq 4pep Length
174 type PROTEIN Struct Unchecked
Input File /opt/Bio/t_coffee/example/sample_aln2.fasta Seq 4ape Length
178 type PROTEIN Struct Unchecked
Input File /opt/Bio/t_coffee/example/sample_aln2.fasta Seq 3app Length
174 type PROTEIN Struct Unchecked
Input File /opt/Bio/t_coffee/example/sample_aln2.fasta Seq 2apr Length
178 type PROTEIN Struct Unchecked
Input File /opt/Bio/t_coffee/example/sample_aln2.fasta Seq 1cms_1 Length
148 type PROTEIN Struct Unchecked
COMPUTE PAIRWISE SIMILARITY [dp_mode: idscore_pair_wise]
[distance_matrix_mode: idscore]
1cms 1cms_1 identity= 19% score=190
1cms 2apr identity= 34% score=340
1cms 3app identity= 31% score=310
1cms 4ape identity= 29% score=290
.......
3app 4pep identity= 34% score=340
4ape 4pep identity= 31% score=310
READ/MAKE LIBRARIES:[3]
lalign_id_pair [method]
[Submit Job][TOT= 15][ 0 %][ELAPSED TIME: 0
sec.][REMAINING TIME: -1073750336 sec.] [Submit Job][TOT= 15][100
%][ELAPSED TIME: 0 sec.][REMAINING TIME: 0 sec.]
[Retrieve Job][TOT= 15][ 0 %][ELAPSED TIME: 0
sec.][REMAINING TIME: 6722352 sec.] [Retrieve Job][TOT= 15][100
%][ELAPSED TIME: 0 sec.][REMAINING TIME: 0 sec.]
slow_pair [method]
.......
Library Total Size: [5142]
#### File Type= WEIGHT Format= tc_weight Name= no | NOT PRODUCED
[WARNING:T-COFFEE:Version_3.84]
WEIGHTED MODE:t_coffee
1cms 0.61
1cms_1 3.32
2apr 0.59
3app 0.49
4ape 0.48
4pep 0.51
MAKE NEIGHBOR JOINING DENDROGRAM
[MODE=nj][DONE]
PROGRESSIVE_ALIGNMENT [Tree Based]
Group 7: [Group 6 ( 1 seq)] with [Group 1 ( 1 seq)]-->[Score=
53][Len= 176]
Group 8: [Group 2 ( 1 seq)] with [Group 7 ( 2 seq)]-->[Score=
8][Len= 196]
......
CLUSTAL FORMAT for T-COFFEE Version_3.84, CPU=0.94 sec, SCORE=34, Nseq=6,
Len=204
1cms ---gevasvpltnyl-dsqyfgkiylgtppqeftv------------------lfdtgss
4pep -----igdeplenyl-dteyfgtigigtpaqdftv------------------ifdtgss
1cms_1 y-tgslhwvpvtv----qqyw----------qftvdsvtisgvvvaceggcqaildtgts
2apr a---gvgtvpmtdygndieyygqvtigtpgkkfnl------------------dfdtgss
4ape s-tgsatttpids-l-ddayitpvqigtpaqtlnl------------------dfdtgss
3app aasgvatntptan---deeyitpvtig--gttlnl------------------nfdtgsa
* * :.: :***::
......
OUTPUT RESULTS
#### File Type= GUIDE_TREE Format= newick Name= sample_aln2.dnd
#### File Type= MSA Format= clustalw Name= sample_aln2.aln
TIP: Change the Width of your MSA with the environement variable
ALN_LINE_LENGTH (all formats)
Command Line: t_coffee /opt/Bio/t_coffee/example/sample_aln2.fasta
[PROGRAM:T-COFFEE]
T-COFFEE Memory Usage: Current= 4.233 Mb, Max= 6.807 Mb
T-COFFEE CPU Usage: 940 millisec
[nostromo@rocks-168 ~]$ |
Further information about t_coffee is available at -
On your cluster head node at /opt/Bio/t_coffee/doc/
