PFSEARCHV2(1)

💖 PFSEARCHV2(1) — the pfsearchV2 glow-up 💖

okay bestie, sit down, hydrate, because we're about to talk about pfsearchV2 from the General Commands Manual section and she is iconic. this is the tool that goes searching through your protein or DNA sequence library looking for segments that match a profile. it's giving "matchmaker but for sequences." 💅

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✨ NAME ✨

pfsearchV2 — search a protein or DNA sequence library for sequence segments matching a profile 🦋

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🌸 SYNOPSIS 🌸

pfsearchV2 [ -abflLrsuxyz ] [ profile-file | - ]
            [ seq-library-file | - ]    [C=#] [W=#]

like, that's the whole vibe. two files (or a - if you're feeling filter-y), some flags, and a couple of parameters. simple. elegant. slay. ✨

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💜 DESCRIPTION 💜

so what does pfsearchV2 actually do, you ask? she compares a query profile against a DNA or protein sequence library. and the result? an unsorted list of profile-sequence matches, written straight to standard output. no cap. 🫶

there are a variety of output formats with different info in them, and you pick your fave via the options -a, -l, -L, -r, -u, -s, -x, -y, -z, and the command-line parameter C=#. choose your own adventure, bestie. 👑

about the inputs:

• profile-file holds a profile in PROSITE format. 📄
• seq-library-file holds a sequence library in EMBL/SWISS-PROT format — that's the one it assumes by default, lowkey — or in Pearson/Fasta format, which you get by using the option -f. 🧬

and the cutest part? pfsearchV2 can be used as a filter if you use - instead of one of the input filenames. pipe girlie behavior. we love to see it. 🌈

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🎀 OPTIONS 🎀

one bullet per flag, all facts, zero skipping, let's goooo:

• -a — report the optimal alignment scores for all sequences, no matter what the cut-off value says. and heads up: this option simultaneously forces DISJOINT=UNIQUE. two-for-one. 💅
• -b — also search the complementary strands of DNA sequences. both strands, because why limit yourself. 🧬
• -f — the input sequence-library is in Pearson/Fasta format. 🍓
• -l — show, by number, the highest cut-off level that the match score exceeded, right there in the output list. 🔢
• -L — show, by character string, the highest cut-off level that the match score exceeded, in the output list. okay so context: the generalized profile format has a text string field that lets you name a cut-off level. -L makes the program display the first two characters of that text string — usually something like "!", "?", "??", etc. — at the beginning of each match description. 🎀
• -r — use raw scores instead of normalized scores for match selection. and just so you know: normalized scores will not be listed in the output. gone. not invited. 💀
• -s — also list the sequences of the matched regions. the output will be a Pearson/Fasta-formatted sequence library. 🦋
• -u — forces DISJOINT=UNIQUE. periodt. ✨
• -x — list profile-sequence alignments in pftools PSA format. 📼
• -y — display the alignments between the profile and the matched sequence regions in a human-friendly format. finally, something readable. 😭
• -z — show the starting and ending position of the matched profile range. the ending position is given as a negative offset from the end of the profile. so like, the range [ 1, -1] means the entire profile. make it make sense? now it does. 🫶

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⭐ PARAMETERS ⭐

• C=# — the cut-off value. this one over-writes the level zero cut-off value specified in the profile. an integer argument gets read as a raw score value, a decimal argument gets read as a normalized score value. and btw, an integer value forces option -r. sneaky but true. 👑
• W=# — the output width. output lines get truncated after W characters. Default: W=132. 📏

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🌈 EXAMPLES 🌈

(1) 🍓

pfsearchV2 -f sh3.prf sh3.seq C=6.0

searches the Pearson/Fasta-formatted protein sequence library sh3.seq for SH3 domains with a cut-off value of 6.0 normalized score units. for the record: sh3.seq contains 20 SH3 domain-containing protein sequences from SWISS-PROT release 32, and sh3.prf contains the PROSITE entry SH3/PS50002. iconic dataset energy. 💅

(2) 🦋

pfsearchV2 -bx ecp.prf CVPBR322 | psa2msa -du | readseq -p -fMSF > ecp.msf

generates a multiple sequence alignment of potential E. coli promoters on both strands of plasmid pBR322. here's the tea: ecp.prf contains a profile for E. coli promoters, and CVPBR322 contains EMBL entry J01749|CVPBR322. the result file ecp.msf can further be processed by GCG programs that accept MSF files as input. pipeline girlie supremacy. 🌈

also see the manual pages of psa2msa. iykyk. 💖

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👑 AUTHOR 👑

Philipp Bucher Philipp.Bucher@isrec.unil.ch 💌

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and that's the whole page, bestie. this was pftools 2.1, dated February 1998 — yes, she's vintage, she's still serving, and she ate. no cap. 🎀💖✨