LAMBDA2_SEARCHP(1)

📦
version 2.0.1 · 5 versions
, in debian trixie, ubuntu questing

✨ LAMBDA2_SEARCHP(1) ✨

okay bestie, pull up a chair 💖 this is the manual page for lambda2_searchp, and it lives in section 1 of the manual. it's the Local Aligner for Massive Biological DatA and honestly? it ate. let's get into it 🫶

🌸 NAME 🌸

lambda2_searchp — the Local Aligner for Massive Biological DatA. that's the whole name. short, iconic, no notes 💅

🎀 SYNOPSIS 🎀

lambda2 searchp [OPTIONS] -q QUERY.fasta -i INDEX.lambda [-o output.m8]

look at her. query in, index in, output optional (but like, you want the output, bestie 🍓).

🦋 DESCRIPTION 🦋

okay so Lambda is a local aligner optimized for many query sequences and it searches in protein space. and here's the flex: it's compatible with BLAST, but it's much faster than BLAST and faster than a whole bunch of other comparable tools too. not me being dramatic, that's literally what the page says 🔥

detailed information lives in the wiki, and you know you're gonna click it:

https://github.com/seqan/lambda/wiki

👑 OPTIONS 👑

💜 the basics 💜

  • -h, --help — show the help message. the classic. the blueprint 💅
  • -hh, --full-help — show the help message but with the advanced options. the director's cut, the extended edition ✨
  • --version — show version info. who are you today? 🪞
  • --copyright — show the long copyright information. the receipts, in full 📜
  • -v, --verbosity INTEGER — how much diagnostic output you get while it's running: 0 is only errors, 1 is the default, 2 is plus run-time, options and statistics. in range [0..2]. Default: 1. lowkey 2 if you're nosy, no judgement 🫶

🧚 Input Options 🧚

  • -q, --query INPUT_FILE — your query sequences 💖 valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression. yes she handles all of them. versatile queen 👑
  • -a, --input-alphabet STRING — the alphabet of the query sequences (specify this to override the auto-detection). Dna sequences will be translated. one of auto, dna5, and aminoacid. Default: auto. she can figure it out herself but you're allowed to tell her 🌸
  • -g, --genetic-code INTEGER — the translation table to use if the input is Dna. see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c for the ids. the default is to use the same table that was used for the index, or 1/CANONICAL if the index was not translated. Default: 0. (yes, 0 is the default value and the fallback logic is described above, keep up bestie 💀)
  • -i, --index INPUT_DIRECTORY — the database index, made by the lambda mkindexp command. valid filetype is: .lambda. this is the mandatory one, don't forget her 🎀

💅 Output Options 💅

  • -o, --output OUTPUT_FILE — the file to hold the reports on hits. (.m* are blastall -m* formats; .m8 is tab-separated, .m9 is tab-separated with comments, .m0 is pairwise format). valid filetypes are: .sam[.*], .m9[.*], .m8[.*], .m0[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression. Default: output.m8. so if you say nothing she just writes output.m8, she's proactive like that ✨
  • --output-columns STRING — print the specified column combination and/or order (.m8 and .m9 outputs only). call -oc help for more details. Default: std. you can customise your little columns, main character energy fr 📊
  • --percent-identity INTEGER — only output matches above this threshold (checked before the e-value check, noted). in range [0..100]. Default: 0.
  • -e, --e-value DOUBLE — only output matches that score below this threshold. in range [0..100]. Default: 1e-04.
  • --bit-score DOUBLE — only output matches that score above this threshold. in range [0..1000]. Default: 0.
  • -n, --num-matches INTEGER — print at most this number of matches per query. in range [1..10000]. Default: 256. rationing the matches, we love a boundary-setter 💅
  • --sam-with-refheader BOOL — BAM files require all subject names to be written to the header. for SAM this is not required, so Lambda does not automatically do it, to save space (especially for a protein database, this is a lot!). if you still want them with SAM, e.g. for better BAM compatibility, use this option. one of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: off.
  • --sam-bam-seq STRING — for BLASTX and TBLASTX the matching protein sequence is "untranslated" and positions retransformed to the original sequence. for BLASTP and TBLASTN there is no DNA sequence so a * is written to the SEQ column. the matching protein sequence can be written as an optional tag, see --sam-bam-tags. if set to uniq then the sequence is omitted iff it is identical to the previous match's subsequence. one of always, uniq, and never. Default: uniq.
  • --sam-bam-tags STRING — write the specified optional columns to the SAM/BAM file. call --sam-bam-tags help for more details. Default: AS NM ae ai qf.
  • --sam-bam-clip STRING — whether to hard-clip or soft-clip the regions beyond the local match. soft-clipping retains the full sequence in the output file, but obviously uses more space. one of hard and soft. Default: hard. hard clip = tidy, soft clip = keeps everything, pick your fighter 🦋

🌈 General Options 🌈

  • -t, --threads INTEGER — number of threads to run concurrently. Default: autodetected. she'll figure out how many cores you have and go feral with them 🔥

🌱 Seeding / Filtration 🌱

  • --adaptive-seeding BOOL — grow the seed if it has too many hits (low complexity filter). one of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on.
  • --seed-length INTEGER — length of the seeds. in range [3..50]. Default: 10.
  • --seed-offset INTEGER — offset for seeding (if unset = seed-length/2). in range [1..50]. Default: 5.
  • --seed-delta INTEGER — maximum seed distance. in range [0..1]. Default: 1.
  • --seed-delta-increases-length BOOL — seed delta increases the min. seed length (for affected seeds). one of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: off.
  • --seed-half-exact BOOL — allow errors only in the second half of the seed. one of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on. half-exact, half-chaotic, it's giving balance ⚖️

🙈 Miscellaneous Heuristics 🙈

  • --pre-scoring INTEGER — evaluate the score of a region NUM times the size of the seed before extension (0 -> no pre-scoring, 1 -> evaluate seed, n -> area around seed, as well; default = 1 if no reduction is used). in range [1..10]. Default: 2.
  • --pre-scoring-threshold DOUBLE — minimum average score per position in the pre-scoring region. in range [0..20]. Default: 2.
  • --filter-putative-duplicates BOOL — filter hits that will likely duplicate a match already found. one of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on.
  • --filter-putative-abundant BOOL — if the maximum number of matches per query are found already, stop searching if the remaining realm looks unfeasible. one of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on.
  • --merge-putative-siblings BOOL — merge seed from one region, stop searching if the remaining realm looks unfeasable. one of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on.

🍓 Scoring 🍓

  • -s, --scoring-scheme INTEGER — use '45' for Blosum45; '62' for Blosum62 (default); '80' for Blosum80. Default: 62.
  • --score-gap INTEGER — score per gap character. in range [-1000..1000]. Default: -1.
  • --score-gap-open INTEGER — additional cost for opening a gap. in range [-1000..1000]. Default: -11.

🚀 Extension 🚀

  • -x, --x-drop INTEGER — stop Banded extension if score x below the maximum seen (-1 means no xdrop). in range [-1..1000]. Default: 30.
  • -b, --band INTEGER — size of the DP-band used in extension (-3 means log2 of query length; -2 means sqrt of query length; -1 means full dp; n means band of size 2n+1). in range [-3..1000]. Default: -3. the negative numbers are vibes-based shortcuts and honestly? iconic 💫
  • -m, --extension-mode STRING — choice of extension algorithms. one of auto, xdrop, and fullSerial. Default: auto.

🌟 TUNING 🌟

okay so real talk bestie, tuning the seeding parameters and (de)activating alphabet reduction has a strong influence on both speed and sensitivity. this is the part where you actually change the vibes of your search. the page recommends the following alternative profiles for protein searches:

  • fast (high similarity): --seed-delta-increases-length on
  • sensitive (lower similarity): --seed-offset 3

for further information see the wiki:

https://github.com/seqan/lambda/wiki

lambda2 searchp Copyright: 2013-2019 Hannes Hauswedell, released under the GNU AGPL v3 (or later); 2016-2019 Knut Reinert and Freie Universität Berlin, released under the 3-clause-BSDL.

SeqAn Copyright: 2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.

in your academic works please cite: Hauswedell et al (2014); doi: 10.1093/bioinformatics/btu439 — cite your sources bestie, it's the least you can do 🙏

for full copyright and/or warranty information see --copyright.

fr fr, that's the whole page. nothing skipped, nothing summarised, every flag accounted for 💖

and that's a wrap on lambda2 searchp 2.0.1, dated Nov 28 2024 🎀 she's serving, she's fast, she's BLAST-compatible, and she's yours. go align something gorgeous, bestie 💅✨🦋

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