Removing gi# from a bunch of sequences?

joeytogo · Post by **joeytogo** » Fri Oct 29, 2010 5:24 pm

Hi,
I would like to remove all but the accession #(ie:NP_721220.1), species (ie:[Strept mut]), and the sequence of course.

starting with this
>gi|24379265|ref|NP_721220.1| excinuclease ABC subunit B [Strept mut]
MIDRKDNNQFHLVSKYEPSGDQPEAIEALVDNIEGGEKAQILKGATGTGKTYTMSQVIQKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV

ending up with this
>NP_721220.1 [Strept mut]
MIDRKDNNQFHLVSKYEPSGDQPEAIEALVDNIEGGEKAQILKGATGTGKTYTMSQVIQKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV

Ideally I would like to keep the accession # and replace .1 [Genus species] with the 1st letter of the genus and the first three of the species.
Like this:
ending up with this
>NP_721220.Smu
MIDRKDNNQFHLVSKYEPSGDQPEAIEALVDNIEGGEKAQILKGATGTGKTYTMSQVIQKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV

Is this possible to do in one step of replacing?

Thank you so much,
Joseph Boggs

example data below

>gi|24379265|ref|NP_721220.1| excinuclease ABC subunit B [Streptococcus mutans UA159]
MIDRKDNNQFHLVSKYEPSGDQPEAIEALVDNIEGGEKAQILKGATGTGKTYTMSQVIQKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|290580728|ref|YP_003485120.1| excinuclease ABC subunit B [Streptococcus mutans NN2025]
MIDRKDNNQFHLVSKYEPSGDQPEAIEALVDNIEGGEKAQILKGATGTGKTYTMSQVIQKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|306831686|ref|ZP_07464843.1| excision endonuclease subunit UvrB [Streptococcus gallolyticus subsp. gallolyticus TX20
MIDRVENNQFKLVSKYQPSGDQPEAIEALVDNIEGGEKAQILLGATGTGKTYTMSQVIAKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|288905600|ref|YP_003430822.1| excinuclease ABC (subunit B) [Streptococcus gallolyticus UCN34]
MIDRIENNQFKLVSKYQPSGDQPEAIEALVDNIEGGEKAQILLGATGTGKTYTMSQVIAKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|306833826|ref|ZP_07466951.1| excision endonuclease subunit UvrB [Streptococcus bovis ATCC 700338]
MIDRVENNQFKLVSKYQPSGDQPEAIEALVDNIEGGEKAQILLGATGTGKTYTMSQVIAKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|228477022|ref|ZP_04061660.1| excinuclease ABC subunit B [Streptococcus salivarius SK126]
MIDRKEDNQFHLVSKYEPSGDQPQAIEALVDNIEGGEKAQILKGATGTGKTYTMSQVIQRVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDFYQPEAYVPSSDTYIEKDSSV
>gi|22537607|ref|NP_688458.1| excinuclease ABC subunit B [Streptococcus agalactiae 2603V/R]
MIDRKDTNRFKLVSKYSPSGDQPQAIETLVDNIEGGEKAQILKGATGTGKTYTMSQVIAQVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|77409684|ref|ZP_00786351.1| excinuclease ABC, B subunit [Streptococcus agalactiae COH1]
MIDRKDTNRFKLVSKYSPSGDQPQAIETLVDNIEGGEKAQILKGATGTGKTYTMSQVIAQVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|76787746|ref|YP_330102.1| excinuclease ABC subunit B [Streptococcus agalactiae A909]
MIDRKDTNRFKLVSKYSPSGDQPQAIETLVDNIEGGEKAQILKGATGTGKTYTMSQVIAQVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|171779931|ref|ZP_02920835.1| hypothetical protein STRINF_01718 [Streptococcus infantarius subsp. infantarius ATCC BA
MIDRIENNHFKLVSKYEPSGDQPQAIETLVNNIEGGEKAQILLGATGTGKTYTMSQVIAKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|116628195|ref|YP_820814.1| excinuclease ABC subunit B [Streptococcus thermophilus LMD-9]
MKGKTMIDRKEDNQFHLVSKYEPSGDQPQAIETLVDNIKGGEKAQILKGATGTGKTYTMSQVIQRVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIE
>gi|251782717|ref|YP_002997020.1| excinuclease ABC subunit B [Streptococcus dysgalactiae subsp. equisimilis GGS_124]
MIDKRDDKPFHLVSKYEPSGDQPQAIETLVDNIEGGEKAQILLGATGTGKTYTMSQVINKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|55821473|ref|YP_139915.1| excinuclease ABC subunit B [Streptococcus thermophilus LMG 18311]
MKGKTMIDRKEDNQFHLVSKYEPSGDQPQAIETLVDNIKGGEKAQILKGATGTGKTYTMSQVIQRVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIE
>gi|222153289|ref|YP_002562466.1| excinuclease ABC subunit B [Streptococcus uberis 0140J]
MIDRRDENTFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILLGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|223932268|ref|ZP_03624271.1| excinuclease ABC, B subunit [Streptococcus suis 89/1591]
MINRNTENQFKLVSKYSPSGDQPQAIETLVDNIEGGEKAQILMGATGTGKTYTMSQVIARVNKPTLVIAHNKTLAGQLYSEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|146320885|ref|YP_001200596.1| excinuclease ABC subunit B [Streptococcus suis 98HAH33]
MINRNTENQFKLVSKYAPSGDQPQAIETLVDNIEGGEKAQILMGATGTGKTYTMSQVIARVNKPTLVIAHNKTLAGQLYSEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|289168043|ref|YP_003446312.1| excinuclease ABC-subunit B [Streptococcus mitis B6]
MINRITDNQFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|225860928|ref|YP_002742437.1| excinuclease ABC subunit B [Streptococcus pneumoniae Taiwan19F-14]
MINRITDNKFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|225868289|ref|YP_002744237.1| UvrABC system protein B (UvrB protein) [Streptococcus equi subsp. zooepidemicus]
MIDKRDFKAFKLVSKYDPSGDQPQAIEALVDNIEGGEKAQILLGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|15903161|ref|NP_358711.1| excinuclease ABC subunit B [Streptococcus pneumoniae R6]
MINHITDNQFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|307704944|ref|ZP_07641835.1| excinuclease ABC, B subunit [Streptococcus mitis SK597]
MINRITDNQFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|149012289|ref|ZP_01833358.1| excinuclease ABC, B subunit [Streptococcus pneumoniae SP19-BS75]
MINHITDNQFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|307708786|ref|ZP_07645248.1| excinuclease ABC, B subunit [Streptococcus mitis NCTC 12261]
MITRITDNQFKLVSKYEPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|270292807|ref|ZP_06199018.1| excinuclease ABC, B subunit [Streptococcus sp. M143]
MINRITDNQFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|15901100|ref|NP_345704.1| excinuclease ABC subunit B [Streptococcus pneumoniae TIGR4]
MINHITDNQFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|307709471|ref|ZP_07645928.1| excinuclease ABC, B subunit [Streptococcus mitis SK564]
MINRITDNQFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|306829598|ref|ZP_07462788.1| excision endonuclease subunit UvrB [Streptococcus mitis ATCC 6249]
MINRITDNKFKLVSKYEPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|225856905|ref|YP_002738416.1| excinuclease ABC subunit B [Streptococcus pneumoniae P1031]
MINHITDNQFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|195978380|ref|YP_002123624.1| excinuclease ABC subunit B [Streptococcus equi subsp. zooepidemicus MGCS10565]
MIDKRDFKAFKLVSKYAPSGDQPQAIEALVDNIESGEKAQILLGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|153854|gb|AAA27020.1| uvs402 protein [Streptococcus pneumoniae]
MERGILMINHITDNQFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYI
>gi|293365540|ref|ZP_06612249.1| excision endonuclease subunit UvrB [Streptococcus oralis ATCC 35037]
MINRITDNKFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|306825137|ref|ZP_07458479.1| excision endonuclease subunit UvrB [Streptococcus sp. oral taxon 071 str. 73H25AP]
MINRITDNKFKLVSKYEPSGDQPQAIERLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|225870778|ref|YP_002746725.1| UvrABC system protein B (UvrB protein) [Streptococcus equi subsp. equi 4047]
MIDKRDFKAFKLVSKYAPSGDQPQAIETLVDNIEGGEKAQILLGATGTGKTYTMSQVISKVNKPTLVVAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|302023818|ref|ZP_07249029.1| excinuclease ABC subunit B [Streptococcus suis 05HAS68]
MINRNTENQFKLVSKYSPSGDQPQAIETLVDNIEGGEKAQILMGATGTGKTYTMSQVIARVNKPTLVIAHNKTLAGQLYSEFNALFPQNAVEYFVSYSDYYQPEAYVPSSDTYIEKDSSS
>gi|169833714|ref|YP_001694670.1| excinuclease ABC subunit B [Streptococcus pneumoniae Hungary19A-6]
MINHITDNQFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|149019230|ref|ZP_01834592.1| excinuclease ABC subunit B [Streptococcus pneumoniae SP23-BS72]
MINHITDNQFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|296876387|ref|ZP_06900439.1| excision endonuclease subunit UvrB [Streptococcus parasanguinis ATCC 15912]
MINRVTDNKFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVIAQVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|148993848|ref|ZP_01823250.1| excinuclease ABC, B subunit [Streptococcus pneumoniae SP9-BS68]
MINHITDNQFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|307706695|ref|ZP_07643501.1| excinuclease ABC, B subunit [Streptococcus mitis SK321]
MINRITDNQFKLVSKYQPSGDQPQAIKQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|301794321|emb|CBW36746.1| UvrABC system protein B (UvrB protein) [Streptococcus pneumoniae INV104]
MINHITDNQFKLVSKYQPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|303254266|ref|ZP_07340375.1| excinuclease ABC subunit B [Streptococcus pneumoniae BS455]
MINHITDNQFKLVSKYQPSGDQLQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|262282394|ref|ZP_06060162.1| excinuclease ABC subunit B [Streptococcus sp. 2_1_36FAA]
MINRITDNKFELISKYEPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVIAQVNKPTLVIAHNKTLAGQLYGEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|125718171|ref|YP_001035304.1| excinuclease ABC subunit B [Streptococcus sanguinis SK36]
MINRITDNKFELVSKYKPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVIAQVNKPTLVIAHNKTLAGQLYGEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|157149718|ref|YP_001450327.1| excinuclease ABC subunit B [Streptococcus gordonii str. Challis substr. CH1]
MINRITDNKFELISKYEPSGDQPQAIEQLVDNIEGGEKAQILMGATGTGKTYTMSQVIAQVNKPTLVIAHNKTLAGQLYGEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|21910532|ref|NP_664800.1| excinuclease ABC subunit B [Streptococcus pyogenes MGAS315]
MIDKRDDKPFKLKSKYKPSGDQPQAIESLVDNIEGGEKAQILLGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|71903721|ref|YP_280524.1| excinuclease ABC subunit B [Streptococcus pyogenes MGAS6180]
MIDKRDDKPFKLKSKYKPSGDQPQAIESLVDNIEGGEKAQILLGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|94990640|ref|YP_598740.1| excinuclease ABC subunit B [Streptococcus pyogenes MGAS10270]
MIDKRDDKPFKLKSKYKPSGDQPQAIESLVDNIEGGEKAQILLGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|139473634|ref|YP_001128350.1| excinuclease ABC subunit B [Streptococcus pyogenes str. Manfredo]
MIDKRDDKPFKLKSKYKPSGDQPQAIESLVDNIEGGEKAQILLGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|50914390|ref|YP_060362.1| excinuclease ABC subunit B [Streptococcus pyogenes MGAS10394]
MIDKRDDKPFKLKSKYKPSGDQPQAIESLVDNIEGGEKAQILLGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|19746295|ref|NP_607431.1| excinuclease ABC subunit B [Streptococcus pyogenes MGAS8232]
MIDKRDDKPFKLKSKYKPSGDQPQAIESLVDNIEGGEKAQILLGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|15675262|ref|NP_269436.1| excinuclease ABC subunit B [Streptococcus pyogenes M1 GAS]
MIDKRDDKPFKLKSKYKPSGDQPQAIESLVDNIEGGEKAQILLGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|94994564|ref|YP_602662.1| excinuclease ABC subunit B [Streptococcus pyogenes MGAS10750]
MIDKRDDKPFKLKSKYKPSGDQPQAIESLVDNIEGGEKAQILLGATGTGKTYTMSQVISKVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|15672544|ref|NP_266718.1| excinuclease ABC subunit B [Lactococcus lactis subsp. lactis Il1403]
MAIERITDNKFELVSKYEPAGDQGEAIAELVDNIENGEKAQILRGATGTGKTYTMSQVIARTGKPTLVMAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSS
>gi|281491028|ref|YP_003353008.1| excinuclease ABC subunit B [Lactococcus lactis subsp. lactis KF147]
MAIERITDNKFELVSKYEPAGDQGEAIAELVDNIENGEKAQILRGATGTGKTYTMSQVIARTGKPTLVMAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSS
>gi|125623401|ref|YP_001031884.1| excinuclease ABC subunit B [Lactococcus lactis subsp. cremoris MG1363]
MAIERITDNKFELVSKYDPAGDQGQAISELVENIENGEKAQILRGATGTGKTYTMSQVIAQTGKPTLVMAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSS
>gi|116511361|ref|YP_808577.1| excinuclease ABC subunit B [Lactococcus lactis subsp. cremoris SK11]
MAIERITDNKFELVSKYDPAGDQGQAISELVENIENGEKAQILRGATGTGKTYTMSQVIAQTGKPTLVMAHNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSS
>gi|256959893|ref|ZP_05564064.1| excinuclease ABC [Enterococcus faecalis Merz96]
MIERETSNTFHLASKYEPAGDQPAAIAELVDGVKGGEKAQILLGATGTGKTFTISNVIQEVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|300862294|ref|ZP_07108374.1| excinuclease ABC, B subunit [Enterococcus faecalis TUSoD Ef11]
MIERETSNTFHLASKYEPAGDQPAAIAELVDGVKGGEKAQILLGATGTGKTFTISNVIQEVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|227517725|ref|ZP_03947774.1| excinuclease ABC subunit B [Enterococcus faecalis TX0104]
MIERETSNTFHLASKYEPAGDQPAAIAELVDGVKGGEKAQILLGATGTGKTFTISNVIQEVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|29375355|ref|NP_814509.1| excinuclease ABC subunit B [Enterococcus faecalis V583]
MIERETSNTFHLASKYEPAGDQPAAIAELVDGVKGGEKAQILLGATGTGKTFTISNVIQEVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|229548705|ref|ZP_04437430.1| excinuclease ABC subunit B [Enterococcus faecalis ATCC 29200]
MIERETSNTFHLASKYEPAGDQPAAIAELVDGVKGGEKAQILLGATGTGKTFTISNVIQEVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|307269815|ref|ZP_07551145.1| excinuclease ABC subunit B [Enterococcus faecalis TX4248]
MIERETSNTFHLASKYEPAGDQPAAIAELVDGVKGGEKAQILLGATGTGKTFTISNVIQEVNKPTLVIAHNKTLAGQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|257875563|ref|ZP_05655216.1| excinuclease ABC [Enterococcus casseliflavus EC20]
MKMIERTTSHEFDLVSKYQPAGDQPEAIHQLVDGVVGGKKAQILLGATGTGKTYTISNLIKEVNKPTLIIAHNKTLAGQLYGEFKDFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDS
>gi|227551701|ref|ZP_03981750.1| excision endonuclease subunit UvrB [Enterococcus faecium TX1330]
MIERDTSRRFELVSKYQPAGDQPEAINQLVDGVVGGKKAQILLGATGTGKTYTISNLIEKVNKPTLIIAHNKTLAGQLYGEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|257869223|ref|ZP_05648876.1| excinuclease ABC [Enterococcus gallinarum EG2]
MKMIERTTSHEFELLSKYQPAGDQPEAIHQLVDGVVGGKKAQILLGATGTGKTYTVSNLIKEVNKPTLIIAHNKTLAGQLYGEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDS
>gi|257882916|ref|ZP_05662569.1| excinuclease ABC [Enterococcus faecium 1,231,502]
MIERDTSRHFELVSKYQPAGDQPEAINQLVDGVVGGKKAQILLGATGTGKTYTISNLIEKVNKPTLIIAHNKTLAGQLYGEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|69248957|ref|ZP_00604830.1| Excinuclease ABC, B subunit [Enterococcus faecium DO]
MIERDTSRHFELVSKYQPAGDQPEAINQLVDGVVGGKKAQILLGATGTGKTYTISNLIEKVNKPTLIIAHNKTLAGQLYGEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|257865936|ref|ZP_05645589.1| excinuclease ABC [Enterococcus casseliflavus EC30]
MKMIERTTSHEFDLVSKYQPAGDQPEAIHQLVDGVVGGKKAQILLGATGTGKTYTISNLIKEVNKPTLIIAHNKTLAGQLYGEFKDFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDS
>gi|294617428|ref|ZP_06697062.1| excinuclease ABC, B subunit [Enterococcus faecium E1679]
MIERDTSRHFELVSKYQPAGDQPEAINQLVDGVVGGKKAQILLGATGTGKTYTISNLIEKVNKPTLIIAHNKTLAGQLYGEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSV
>gi|304386222|ref|ZP_07368555.1| excision endonuclease subunit UvrB [Pediococcus acidilactici DSM 20284]
MNGGKIMIEREENRQFELVSKYQPTGDQPTAIKQLVDGIQKGEKEQILLGATGTGKTFTISNVIQQVNKPTLILSHNKTLAGQLYGEFKQFFPNNAVEYFVSYYDYYQPEAYVPSSDTYI
>gi|116333297|ref|YP_794824.1| excinuclease ABC subunit B [Lactobacillus brevis ATCC 367]
MIDRQTDRAFDLVSKYQPTGDQPEAINQLTHGIEAGEKAQILLGATGTGKTFTISNVIKNVNKPTLVLSHNKTLAGQLYGEFKQFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|270290697|ref|ZP_06196921.1| excinuclease ABC, B subunit [Pediococcus acidilactici 7_4]
MIEREENRQFELVSKYQPTGDQPTAIKQLVDGIQKGEKEQILLGATGTGKTFTISNVIQQVNKPTLILSHNKTLAGQLYGEFKQFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|227510643|ref|ZP_03940692.1| excision endonuclease subunit UvrB [Lactobacillus brevis subsp. gravesensis ATCC 27305]
MIERENNHKFDLVSSYQPTGDQPQAIKKLVNGVDDGKKAQILLGATGTGKTFTISNVIAQVNKPTLVLSHNKTLAGQLYGEFKEFFPHNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|227513658|ref|ZP_03943707.1| excision endonuclease subunit UvrB [Lactobacillus buchneri ATCC 11577]
MIERENNHKFDLVSSYQPTGDQPQAIKKLVNGVDDGKKAQILLGATGTGKTFTISNVIAQVNKPTLVLSHNKTLAGQLYGEFKEFFPHNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|300214835|gb|ADJ79251.1| UvrABC system protein B [Lactobacillus salivarius CECT 5713]
MIERQADRNFELVSKYSPTGDQPEAIQELTEGIKKGEKAQILMGATGTGKTFTISNVIKNVNKPTLVLAHNKTLAGQLYGEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|268319816|ref|YP_003293472.1| excinuclease ABC, B subunit , UvrABC system [Lactobacillus johnsonii FI9785]
MIRRQKNKKFELVSKFQPAGDQEQAIKKLTDGFEQGEKAQILEGATGTGKTFTMANVIAKLNKPTLVISHNKTLVGQLYGEFKEFFPKNAVDYFVSYYDYYQPEAYVPQSDTYIEKDSSI
>gi|90962150|ref|YP_536066.1| excinuclease ABC subunit B [Lactobacillus salivarius UCC118]
MIERQADRNFELVSKYSPTGDQPEAIQELTEGIKKGEKAQILMGATGTGKTFTISNVIKNVNKPTLVLAHNKTLAGQLYGEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|300361294|ref|ZP_07057471.1| excision endonuclease subunit UvrB [Lactobacillus gasseri JV-V03]
MIRRQKNKKFELVSKFQPAGDQEQAIKKLTDGFENGEKAQILEGATGTGKTFTMANVIAKLNKPTLVISHNKTLVGQLYGEFKEFFPKNAVDYFVSYYDYYQPEAYVPQSDTYIEKDSSI
>gi|184153027|ref|YP_001841368.1| excinuclease ABC subunit B [Lactobacillus reuteri JCM 1112]
MIYRQPDKKFELVSEYKPTGDQPQAINQLTKGIEDGEKAQILLGATGTGKTFTISNVIANVNKPTLILSHNKTLAGQLYGEMKKFFPHNAVEYFVSYYDYYQPEAYVPSSDTYIEKDASI
>gi|42518788|ref|NP_964718.1| excinuclease ABC subunit B [Lactobacillus johnsonii NCC 533]
MIRRQKNKKFELVSKFQPAGDQEQAIKKLTDGFEQGEKAQILEGATGTGKTFTMANVIAKLNKPTLVISHNKTLVGQLYGEFKEFFPKNAVDYFVSYYDYYQPEAYVPQSDTYIEKDSSI
>gi|227889627|ref|ZP_04007432.1| excision endonuclease subunit UvrB [Lactobacillus johnsonii ATCC 33200]
MIRRQKNKKFELVSKFQPAGDQEQAIKKLTDGFEQGEKAQILEGATGTGKTFTMANVIAKLNKPTLVISHNKTLVGQLYGEFKEFFPKNAVDYFVSYYDYYQPEAYVPQSDTYIEKDSSI
>gi|238853234|ref|ZP_04643619.1| excinuclease ABC subunit B [Lactobacillus gasseri 202-4]
MIRRQKNKKFELVSKFQPAGDQEQAIKKLTDGFEQGEKAQILEGATGTGKTFTMANVIAKLNKPTLVISHNKTLVGQLYGEFKEFFPKNAVDYFVSYYDYYQPEAYVPQSDTYIEKDSSI
>gi|301301267|ref|ZP_07207422.1| excinuclease ABC, B subunit [Lactobacillus salivarius ACS-116-V-Col5a]
MIERQADRNFELVSKYSPTGDQPEAIQELTEGIKKGEKAQILMGATGTGKTFTISNVIKNVNKPTLVLAHNKTLAGQLYGEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|227891173|ref|ZP_04008978.1| excinuclease ABC subunit B [Lactobacillus salivarius ATCC 11741]
MGGFDVIERQADRNFELVSKYSPTGDQPEAIQELTEGIKKGEKAQILMGATGTGKTFTISNVIKNVNKPTLVLAHNKTLAGQLYGEFKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIE
>gi|226820640|ref|ZP_03809759.1| excinuclease ABC subunit B [Lactobacillus gasseri MV-22]
MIRRQKNKKFELVSKFQPAGDQEQAIKKLTDGFEQGEKAQILEGATGTGKTFTMANVIAKLNKPTLVISHNKTLVGQLYGEFKEFFPKNAVDYFVSYYDYYQPEAYVPQSDTYIEKDSSI
>gi|194468167|ref|ZP_03074153.1| excinuclease ABC, B subunit [Lactobacillus reuteri 100-23]
MIYRQPDKKFELVSEYKPTGDQPQAINQLTKGIEDGEKAQILLGATGTGKTFTISNVIANVNKPTLILSHNKTLAGQLYGEMKKFFPHNAVEYFVSYYDYYQPEAYVPSSDTYIEKDASI
>gi|81428136|ref|YP_395135.1| excinuclease ABC subunit B [Lactobacillus sakei subsp. sakei 23K]
MIDRQNDNLFDLVAPYEPAGDQPAAIETLTKNFEAGAKAQVLMGATGTGKTFTMSNVIKNLNKPTLIISHNKTLAGQLYAEFKQFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|28377628|ref|NP_784520.1| excinuclease ABC subunit B [Lactobacillus plantarum WCFS1]
MIDRVDNNHFDLVSDYQPTGDQPQAIQQLTAGIESGEKEQILLGATGTGKTFTISNVIAKVNKPTLILSHNKTLAGQLYGEFKKFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSAI
>gi|148543619|ref|YP_001270989.1| excinuclease ABC subunit B [Lactobacillus reuteri DSM 20016]
MKLRFHFILFNCDVREEILLIYRQPDKKFELVSEYKPTGDQPQAINQLTKGIEDGEKAQILLGATGTGKTFTISNVIANVNKPTLILSHNKTLAGQLYGEMKKFFPHNAVEYFVSYYDYY
>gi|116629946|ref|YP_815118.1| excinuclease ABC subunit B [Lactobacillus gasseri ATCC 33323]
MIRRQKNKKFELVSKFQPAGDQEQAIKKLTDGFEQGEKAQILEGATGTGKTFTMANVIAKLNKPTLVISHNKTLVGQLYGEFKEFFPKNAVDYFVSYYDYYQPEAYVPQSDTYIEKDSSI
>gi|227545102|ref|ZP_03975151.1| excision endonuclease subunit UvrB [Lactobacillus reuteri CF48-3A]
MKLRFHFILFNCDVREEFLLIYRQPDKKFELVSEYKPTGDQPQAINQLTKGIEDGEKAQILLGATGTGKTFTISNVIANVNKPTLILSHNKTLAGQLYGEMKKFFPHNAVEYFVSYYDYY
>gi|133930529|gb|ABO43835.1| excinuclease ABC, B subunit [Lactobacillus reuteri]
MIYRQPDKKFELVSEYKPTGDQPQAINQLTKGIEDGEKAQILLGATGTGKTFTISNVIANVNKPTWILSHNKTLAGQLYGEMKKFFPHNAVEYFVSYYDYYQPEAYVPSSDTYIEKDASI
>gi|116492251|ref|YP_803986.1| excinuclease ABC subunit B [Pediococcus pentosaceus ATCC 25745]
MIKRENDREFELVSKYQPTGDQPTAINELVDGIKSGEKEQILLGATGTGKTFTISNVIQKVNKPTLILSHNKTLAGQLYGEFKQFFPNNAVEYFVSYYDYYQPEAYVPSSDTYIEKDSSI
>gi|227535570|ref|ZP_03965619.1| excision endonuclease subunit UvrB [Lactobacillus paracasei subsp. paracasei ATCC 25302
MSMIERIADRKFDLVSPYQPAGDQPQAIAKLTKGFEEGKKEQILLGATGTGKTFTMSNIIANLNKPTLILSHNKTLAGQLYGEFKEFFPHNAVEYFVSYYDYYQPEAYVPSTDTYIEKDS
>gi|116494463|ref|YP_806197.1| excinuclease ABC subunit B [Lactobacillus casei ATCC 334]
MIERIADRKFDLVSPYQPAGDQPQAIAKLTKGFEEGKKEQILLGATGTGKTFTMSNIIANLNKPTLILSHNKTLAGQLYGEFKEFFPHNAVEYFVSYYDYYQPEAYVPSTDTYIEKDSAI
>gi|229551769|ref|ZP_04440494.1| excision endonuclease subunit UvrB [Lactobacillus rhamnosus LMS2-1]
MIERIADRKFDLVSPYKPAGDQPQAIAKLTKGFEEGKKAQILLGATGTGKTFTMSNIIANLNKPTLILSHNKTLAGQLYGEFKEFFPHNAVEYFVSYYDYYQPEAYVPSTDTYIEKDSAI
>gi|116617516|ref|YP_817887.1| excinuclease ABC subunit B [Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293]
MIERQIEHEFEIKSKYEPTGDQPKAIEKLVGGINNHVKEQILLGATGTGKTFTISNVIKEVKKPTLVLSHNKTLAGQLYGELKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTFIEKDSAV
>gi|199597263|ref|ZP_03210694.1| excinuclease ABC subunit B [Lactobacillus rhamnosus HN001]
MIERIADRKFDLVSPYKPAGDQPQAIAKLTKGFEEGKKAQILLGATGTGKTFTMSNIIANLNKPTLILSHNKTLAGQLYGEFKEFFPHNAVEYFVSYYDYYQPEAYVPSTDTYIEKDSAI
>gi|227529561|ref|ZP_03959610.1| excision endonuclease subunit UvrB [Lactobacillus vaginalis ATCC 49540]
MIYRQPHKNFELVSDYKPTGDQPEAIKELTTGIEKGEKAQILLGATGTGKTFTISNVIAKVNKPTLILSHNKTLAGQLYSEMKKFFPHNAVEYFVSYYDYYQPEAYVPSSDTYIEKDASI
>gi|227432640|ref|ZP_03914616.1| excision endonuclease subunit UvrB [Leuconostoc mesenteroides subsp. cremoris ATCC 1925
MIERQIEHEFEIKSKYEPTGDQPQAIEKLVGGINNHVKEQILLGATGTGKTFTISNVIKEVKKPTLVLSHNKTLAGQLYGELKEFFPNNAVEYFVSYYDYYQPEAYVPSSDTFIEKDSAV
[/b]

ben_josephs · Post by **ben_josephs** » Fri Oct 29, 2010 6:34 pm

It really wasn't necessary to post 200 lines (22KB) of redundant sample data.

You said you wanted the first three letters of the species, but your example showed only two. Assuming the latter:

Use Posix regular expression syntax:

Configure | Preferences | Editor

[X] Use POSIX regular expression syntax

Find what: ^>gi\|[^|]*\|[^|]*\|([^|]*)\.1\|[^|]*\[(.)[^ ]* (..).*
Replace with: >\1.\2\3

[X] Regular expression

Replace All

joeytogo · Post by **joeytogo** » Tue Nov 09, 2010 9:59 pm

HI Ben, I want to keep 1 species and 3 genus letters. Thanks for the code below. It gives 1 species and 2 genus letters. I've been using posix.

Find what: ^>gi\|[^|]*\|[^|]*\|([^|]*)\.1\|[^|]*\[(.)[^ ]* (..).*
Replace with: >\1.\2\3

What I've tried:
Replace with: >\1.\2\4
Replace with: >\1.\2\3\4

Thanks, joey

ben_josephs · Post by **ben_josephs** » Tue Nov 09, 2010 10:21 pm

Find what: ^>gi\|[^|]*\|[^|]*\|([^|]*)\.1\|[^|]*\[(.)[^ ]* (...).*
Replace with: >\1.\2\3