Example command lines

Simple BlastX-like run

1. Download pre-formatted UniprotSprot from Pre-built-Database-Indexes.
2. Select your query file or take this example.
3. Run bin/lambda -q /path/to/1k_long_reads.fna -d /path/to/uniprot_sprot.fasta.gz

You will see something like this:

LAMBDA - the Local Aligner for Massive Biological DatA
======================================================
Version 0.9.4

Loading Subj Sequences... done.
Loading Subj Ids... done.
Loading Database Index... done.
Loading Database Masking file... done.
Loading Query Sequences and Ids...translating... done.
Searching and extending hits on-line...progress:
0%  10%  20%  30%  40%  50%  60%  70%  80%  90%  100%
|....:....:....:....:....:....:....:....:....:....|
Number of valid hits:                           77763
Number of Queries with at least one valid hit:    709

Since you did not specify it, the default output file name and -format was used output.m8. Browse the output file with your editor of choice, or less on the command line:

% less output.m8
SHAA001TF       sp|Q00593|ALKJ_PSEOL    31.03   290     191     7       1       849     84      371     2e-34    147
SHAA001TF       sp|Q9WWW2|ALKJ_PSEPU    31.03   290     191     6       1       849     84      371     1e-32    141
SHAA001TF       sp|Q8BJ64|CHDH_MOUSE    24.28   276     205     3       1       819     132     406     1e-20    101
SHAA001TF       sp|Q6UPE0|CHDH_RAT      24.01   279     202     3       1       819     135     409     5e-20   99.0
SHAA001TF       sp|Q8NE62|CHDH_HUMAN    24.28   276     205     3       1       819     130     404     6e-19   95.5
SHAA002TR       sp|A7MD48|SRRM4_HUMAN   27.78   216     144     5       25      657     403     611     1e-06   54.7
SHAA002TR       sp|O13547|CCW14_YEAST   28.95   114     76      1       382     723     105     213     0.070   38.9
SHAA004TF       sp|P0A916|OMPW_SHIFL    50.43   115     49      2       389     733     1       107     8e-23    108
SHAA004TF       sp|P0A915|OMPW_ECOLI    50.43   115     49      2       389     733     1       107     8e-23    108
SHAA004TF       sp|P17266|OMPW_VIBCH    52.21   113     45      2       410     733     4       112     2e-22    107
SHAA004TF       sp|Q8ZP50|OMPW_SALTY    50.43   115     49      2       389     733     1       107     7e-21    102
SHAA004TF       sp|Q8Z7E2|OMPW_SALTI    50.43   115     49      2       389     733     1       107     7e-21    102
[...]

NOTE: Because Lambda uses multiple threads by default, the output is not guaranteed to be in the sameorder (however matches of one query sequence always appear en-bloc and sorted by e-value).