spaln - mapping and alignment of cDNA/protein sequences onto
genomic sequence or rapid homology search against protein sequence database
and (semi)global alignment
spaln -WGenome.bk[n|p] -K[D|P] [W_Options] Genome.mfa(.gz)
spaln -WProsDb.bka -KA [W_Options] ProteinSeqenceDB.faa(.gz)
spaln [-Q[0|1|2|3]] [R_options] Genome_segment [cDNA|protein]_queries
spaln -Q[4|5|6|7] -dGenome [R_options] [cDNA|protein]_queries
spaln -Q[4|5|6|7] -aProsDb [R_options] Genomic_segment
spaln -Q[4|5|6|7] -aProsDb [R_options] protein_queries
spaln -Q[4|5|6|7] [R_options] Genome.mfa [cDNA|protein]_queries
spaln -Q[4|5|6|7] [R_options] ProsDb.faa protein_queries
spaln is a stand-alone program that maps and aligns a set
of cDNA/protein sequences onto a genomic sequence. From version 1.4,
spaln supports a combination of protein sequence database and a given
genomic segment. From version 2.2, it also supports rapid similarity search
of protein sequences against a protein sequence database followd by ordinary
alignment.
Spaln runs with relatively small internal memory, making it
feasible to search a whole mammalian genome in a single job on a
conventional computer.
- spaln -Wddignm.bkn -KD
-Xk10 -Xb8192 ddignm.mfa
- Make the block index table 'ddignm.bkn' of the genomic sequence
'ddignm.mfa' in multi-fasta format with the word size of 10 nucleotides
and the block size of 8192.
- spaln -O1 'chr1.fa
10001 40000 <' cdna.fa
- Align the cDNA sequence 'cdna.fa' onto the genomic segment of 'chr1.fa'
within the range from the 10001-th to the 40000-th nucleotide of the
complementary strand in the semi-global mode.
- spaln -Q7 -LS -t10
-dddignm ddicdna.mfa > ddi.exon
- Report the gene structures corresponding to individual cDNAs in
'ddicdna.mfa'. The local alignment mode is used and the results are
written in 'ddi.exon' in the exon-oriented format. The computation
proceeds with 10 threads in parallel.
- spaln -Q7 -O5 -XG1M
-yX -TMus -ommu.intron -dmmugnm 'ratcdna.mfa (1 20)'
- Cross-species comparison between the genome 'mmugnm' and the cDNAs in
'ratcdna.mfa' from the first to the 20-th entries. The maximal expected
gene size is reset to 1 Mbp. The outputs go to 'mmu.intron' in the
intron-oriented format. The tetrapod-specific parameter set is used.
- spaln -Q7 -O0
-Tarabthal -aSwiss -oyour_genes.gff3 your_genomic_segment
- A set of ORFs in the genomic segment are translated and rapidly searched
against the protein database, and then the best-hit sequence is used as
the template of the spliced alignment to infer the organization of the
gene located in the relevant genomic region. The output is shown in Gff3
gene format. The dicot-specific parameter set is used.
- spaln -Q4 -O0 -aSwiss
-M4 -t10 aa_queries > output
- Find up to four SwissProt sequences most similar to each query sequence,
and report global alignment statistics. To show alignment themselves, use
-O1 option in stead of -O0. The computation proceeds with 10 threads in
parallel.
Conventions: #: number; $: string; default values in ()
(default for DNA, with -yX option, default for protein)
- -K$
- Format the genomic sequence for DNA ($=D) or protein ($=P) queries, or
format the protein database sequences ($=A) for rapid search of template.
- -Xk#
- Word size (11 for DNA, 5 for protein)
- -Xb#
- Block size (4096)
- -XG#
- Maximum gene size (262144)
- -Xa#
- Abundance factor (10)
- -Xs#
- Shifts between adjacent seeds (k)
- -C#
- NCBI transl_table number indicating the genetic code (1)
- -H#
- Minimum alignment score for report (35)
- -LS
- Smith-Waterman-type local alignment
- -M[#]
- Multiple loci (0)
#=empty: Multiple loci maximally up to 4
#=0: Single locus
#=1: Re-search unaligned parts
#>1: Multiple loci maximally up to #
- -O[#]
- Output format (4)
#=0: GFF3 format (gene) in genome vs [cDNA|protein] mode
#=0: Alignment statistics in protein vs protein mode
#=1: Alignment
#=2: GFF3 format (match)
#=3: Bed format
#=4: Exon-oriented format similar to output of megablast -D 3
#=5: Intron-oriented output
#=6: Concatenated exon sequence
#=7: Translated amino-acid sequence
#=8: Mapping (block) information only. Use with -Q4
#=12: Output the same information as -O4 in binary formats
- -Q[#]
- Select algorithm (3)
0<=#<=3: Genomic segment in the fasta format given
by the first argument vs. cdna/protein given by the second argument
4<=#<=7: Genome mapping and alignment
#=0,4: DP procedure without HSP search
#=1-3,5-7: Recursive HSP searches up to the level of (# % 4)
- -R$
- Read block index table from the file $
- -S[#]
- Specify the orientation of query (0)
0: depend on the query annotation
1: forward direction only
2: reverse direction only
3: both directions;
- -T$
- Specify the species (in combination with the -yS option for cDNA
query)
- -U
- Map/align without splicing
- -V#
- Minimum space to induce the Hirschberg's algorithm (16M)
- -W$
- Write block index table to file $
- -i[a|p]
- Paired-end reads as the queries from a single or two files
-ia: 5' and 3' matching pairs must appear alternatively
in a file
-ip: 5' and 3' matching pairs must appear in the same order in the two
files
- -o$
- Destination of output file (stdout)
- -pa
- Suppress trimming of terminal polyA or polyT sequence
- -pq
- Suppress some outputs to stderr
- -pw
- Report the result irrespective of the alignment score
- -u#
- Gap-extension penalty (3, 2, 2)
- -v#
- Gap-opening penalty (8, 6, 9)
- -xB$
- Bit pattern of the seeds used for HSP search at level 1
- -xb$
- Bit pattern of the seeds used for HSP search at level 3
- -ya#
- Dinucleotide pairs at the ends of an intron (0)
0: canonical only (GT..AG, GC..AG, AT..AC)
1: relaxed to (GT..AG, GC..AG, AT..AN)
2: #=1 + allow 1 mismatch from GT..AG
3: any;
- -yi#
- Intron penalty (11, 8, 11)
- -yj#
- Incline of long gap penalty (0.6)
- -yk#
- Flex point where the incline of gap penalty changes (7)
- -yl#
- Double affine gap penalty if #=3; affine penalty otherwise
- -ym#
- Score for a nucleotide match (2, 2)
- -yn#
- Penalty for a nucleotide mismatch (6, 2)
- -yo#
- Penalty for in-frame termination codon (100)
- -yp#
- PAM level used in the alignment (third) phase (150)
- -yq#
- PAM level used in the second phase (50)
- -yx#
- Penalty for a frame shift (100)
- -yy#
- Relative contribution of splicing signal (8)
- -yz#
- Relative contribution of coding potential (2)
- -yA#
- Relative contribution of the translational initiation or termination
signal (8)
- -yB#
- Relative contribution of branch point signal (0)
- -yE#
- Minimum exon length (2)
- -yI$
- Intron distribution parameters
- -yJ#
- Relative contribution of the bonus given to a conserved intron
position
- -yL#
- The minimum intron length (20)
- -yS#
- Percent contribution of the species-specific splice signal. if #=0, only
the ubiquitous signal given to the dinucleotide pair at the ends of an
intron is used. By default #=0 for DNA and #=100 for protein queries. -yX
option automatically sets #=100 for DNA and #=30 for protein. -yS
For cDNA queries, use species-specific exon-intron boundary signals. For
protein queries, invoke 'salvage' procedure in phase 1
- -yX
- For a DNA query, this option sets parameter values for cross-species
comparison. Conversely, this option specifies an intra-species mode for a
protein query.
- -yY#
- Relative contribution of length-dependent part of intron penalty (8)
- -yZ#
- Relative contribution of oligomer composition within an intron (0)
(1) "A Space-Efficient and Accurate Method for Mapping and
Aligning cDNA Sequences onto Genomic Sequence", Osamu Gotoh, Nucleic
Acid Res., 36 (8), 2630-2638 (2008).
(2) "Direct Mapping and Alignment of Protein Sequences onto Genomic
Sequence", Osamu Gotoh, Bioinformatics, 24 (21) 2438-2444 (2008).
(3) "Benchmarking spliced alignment programs including Spaln2, an
extended version of Spaln that incorporates additional species-specific
features", Iwata, H. and Gotoh, O.", Nucleic Acids Res., 40 (20)
e161 (2012).
Osamu Gotoh <o.gotoh@aist.go.jp>