FASTBLOCKSEARCH(1)

📦
version 3.5.0 · 5 versions
, in ubuntu resolute, ubuntu stonking

💖 FASTBLOCKSEARCH(1) 💖

okay bestie, gather round, because this is the fastBlockSearch manual page and it's literally iconic 💅 it lives in section 1 of the manual (that's FASTBLOCKSEARCH(1) for the iykyk girlies) and it's about to make your protein block search dreams come true fr fr.

✨ NAME ✨

fastBlockSearch — search loci matching protein block profiles 🧬🔍

🌸 SYNOPSIS 🌸

fastBlockSearch [options] seqs.fa fam.prfl

🦋 DESCRIPTION 🦋

so what does it actually do? it searches hits (matches) of the blocks in the profile given by fam.prfl inside the genomic sequences sitting in seqs.fa. that's the whole vibe. 💫

the hits come out sorted increasingly by score, which means the last displayed hit is the best one found in the region — so if you're the kind of girl who scrolls to the bottom, congrats, you've been doing it right the whole time. no cap. 👑

the format? it's similar to that of the blockscore file (the one that's optionally generated by msa2prfl.pl). it shows you:

  • coordinate 📍
  • strand ➡️
  • mean odds-ratio score 📊
  • specificity of score 🎯
  • and the motif 🧬

and here's the cute part: from the output users can chose regions with matching blocks to perform gene prediction with AUGUSTUS-PPX using the same block profile. so like, you find the hits, you pick the regions, you go do your gene prediction thing. it's giving pipeline energy. 🌈

🔥 EXAMPLE 🔥

> fastBlockSearch --cutoff=1.1 chr4.103M.fa PF00225_seed.prfl

Hits found in chr4 103000000 105000000
Score:207.987
Mult. score:4.83391
1081586 unknown_M[5,13] -       2.32574 5.04633 .....YATRLKNI
1103952 unknown_L       -       4.85363 6.75245 NAKTRIICTITP
1103991 unknown_K       -       8.38065 9.92928 YRDSKLTRILQNSLG
1104375 unknown_J       -       3.96065 6.79408 RSLFILGQVIKKL
1106992 unknown_I       -       9.22487 7.64306 LVDLAGSE
1115567 unknown_H[5,16] -       2.31869 5.58986 .....ESRHYGETKMN
1116319 unknown_G       -       7.34282 8.29425 EIYNETITDLL
1117092 unknown_F       -       5.10694 6.10274 VIPRAIHDIF
1117146 unknown_E       -       9.43596 9.18891 QTASGKTYTM
1117176 unknown_D[1,8]  -       5.73796 6.31532 .GTIFAYG
1117399 unknown_B[1,7]  -       3.59083 5.03059 .CLDRVF
1119420 unknown_A[0,8]  -       4.64107 6.44285 RVRPLNSR.

look at all those hits just lining up. absolutely ate. 💅✨

🎀 OPTIONS 🎀

  • --cutoff=c — this is the minimum for the average log score of the motifs found, and you use it to adjust the sensitivity of the block search. the standard cutoff is 0.7, which is very sensitive — and, lowkey important, it can give many false positive hits for smaller profiles 🙈 so like, sensitive queen but she does exaggerate sometimes.

👑 AUTHORS 👑

Oliver Keller 💜

and that's the whole page, bestie 🫶 FASTBLOCKSEARCH(1) — that's the manual name, you'll see it on both the header and the footer of the original, and the footer is where the source/version and date live too. mwah, go search some blocks. ⭐🎀🌸

📦 where this page comes from