suppose my one file has
>1|lol|hai i am cdfd
dafvshbejndjnudbnjdbyebjcb
bdhbdjndjndmdkmdkldhddjndj
dbdhbndjndjmdklm
sjskndknsknsknks
sbsjksnknsknknklsl
>2|lol|hai ia m cdfd123
jbsjbjbjbjbjbjbjbjbjbj
jkbkkkkkkkkkkkkk
khkkkkkkkkkkkkk
scbjbjbakbqlblabkla
>3lol|hai ia m cdfd3435
jshjhjhjhklbusbikjljsl
skhmsbcjkbkhk;sk=
bsjkhslskksjkljskjls
continue sure that it is a very large file
another file
>1|lol|hai i am cdfd
>2|lol|hai ia m cdfd123
>5lol|hai ia m cdfd6756

so output shud be
1|lol|hai i am cdfd
dafvshbejndjnudbnjdbyebjcb
bdhbdjndjndmdkmdkldhddjndj
dbdhbndjndjmdklm
sjskndknsknsknks
sbsjksnknsknknklsl
>2|lol|hai ia m cdfd123
jbsjbjbjbjbjbjbjbjbjbj
jkbkkkkkkkkkkkkk
khkkkkkkkkkkkkk
scbjbjbakbqlblabkla
>5|lol|i a cdfd7647
akjklsdjljslslkls
ksksjl;vlsjvkd;lsjls
sjsdkvnslnlsjls;lks
sjkdlsjdldsvlsj;;sk;;

csplit -f xyz input_file /^>/ {99}
for mFile in `egrep -l -f reference_file xyz*`
do
  cat ${mFile}
done

but if u have one file like that
>gi|62859953|ref|NP_001017322.1| plexin B2 [Xenopus tropicalis]
MKEKERTKAITEIYLTRLLSVKGTLQQFVDNFFQSVLNSNQVVPPAVKYFFDFLDEQAEKYEIKDEDTVHIWKTNSLSLR
FWVNILKNPHFIFDVHVHQVVDASLSVIAQTFMDACSRTEHKLSRESPSNKLLYAKEISTYKKMVEDYYKGIRQMVQVSD
QDMNTHLAEISRAHTESLNTLVALHQLYQYTNKYYDEIINALEEDPAAQRMQLAYRLQQIAAALENKVTDL
>gi|62859377|ref|NP_001016112.1| O-sialoglycoprotein endopeptidase [Xenopus tropicalis]^Agi|111305744|gb|AAI21531.1| O-sialoglycoprotein endopeptidase [Xenopus tropicalis]

MTIVVGFEGSANKIGVGIIQDGKVLSNPRRTYITPPGQGFMPSDTARHHRSCILDVLQEALEEAKIKPQDVDCVAYTKGP
GMGAPLLSVAIVARTVAQLWKKPLLGVNHCIGHIEMGRLITGAENPSVLYVSGGNTQVIAYSERCYRIFGETIDIAVGNC
LDRFARVLKISNDPSPGYNIEQMAKKGKKFVELPYTVKGMDVSFSGILSYIEDMSHKMLSSGECTPEDLCFSLQETLFSM
LVEITERAMAHCGSQEVLIVGGVGCNVRLQEMMGVMCQERGAKLFATDERFCIDNGAMIAQAGWEMFRSGQVTNLQDSWI
TQRYRTDEVEVTWRD
continuing.....
As first file contains full list of all. proteins..............


and another 2nd file like that......
>gb|AAI30281.1| ABCA8 protein [Homo sapiens]
>ref|XP_001165971.1| PREDICTED: similar to KIAA0822 protein isoform 5 [Pan troglodytes]
>ref|XP_001082492.1| PREDICTED: similar to ATP-binding cassette, sub-family A member 8[Macaca mulatta]
>ref|XP_001165871.1| PREDICTED: similar to KIAA0822 protein isoform 2 [Pan troglodytes]
>ref|XP_001494133.1| PREDICTED: similar to ABCA8 protein [Equus caballus]
continuing.......


so two files have one in common >gb|AAI30281.1| ABCA8 protein [Homo sapiens]
>>gi|114670186|ref|XP_00........contnuing....

So, while taking second file to search for in the first file like this .
u shud have a output like this
>gb|AAI30281.1| ABCA8 protein [Homo sapiens]
MRKRKISVCQQTWALLCKNFLKKWRMKRESLMEWLNSLLLLLCLYIYPHSHQVNDFSSLL
TMDLGRVDTFNESRFSVVYTPVTNTTQQIMNKVASTPFLAGKEVLGLPDEESIKEFTANY
PEEIVRVTFTNTYSYHLKFLLGHGMPAKKEHKDHTAHCYETNEDVYCEVSVFWKEGFVAL
QAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCIISFSSFIYYA
SVNVTRERKRMKALMTMMGLRDSAFWLSWGLLYAGFIFIMALFLALVIRSTQFIILSGFM
VVFSLFLLYGLSLVALAFLMSILVKKSFLTGLVVFLLTVFWGCLGFTSLYRHLPASLEWI
LSLLSPFAFMLGMAQLLHLDYDLNSNAFPHPSDGSNLIVATNFMLAFDTCLYLALAIYFE
KILPNEYGHRRPPLFFLKSSFWSQTQKTDHVALEDEMDADPSFHDSFEQAPPEFQGKEAI
RIRNVTKEYKGKPDKIEALKDLVFDIYEGQITAILGHSGAGKSTLLNILSGLSVPTKGSV
TIYNNKLSEMADLENLSKLTGVCPQSNVQFDFLTVRENLRLFAKIKGILPQEVDKEIFLL
DEPTAGLDPFSRHQVWNLLKERKTDRVILFSTQFMDEADILADRKVFLSQGKLKCAGSSL
FLKKKWGIGYHLSLQLNEICVEENITSLVKQHIPDAKLSAKSEGKLIYTLPLERTNKFPE
>gi|114670186|ref|XP_001165971.1| PREDICTED: similar to KIAA0822 protein isoform 5 [Pan troglodytes]
MRKRKISVCQQTWALLCKNFLKKWRMKRESLMEWLNSLLLLLCLYIYPHSHQVNDFSSLLTMDLGRVDTFNESRFSVVYT
PVTNTTQQIMNKVASIPFLAGKEVLGLPDEESIKEFTANYPEEIVRVTFTNTYSYHLKFLLGHGMPAKKEHKDHTAHCYE
TNEDVYCEVSVFWKEGFVALQAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCLISFSSFIYYA
SVNVTRERKRMKGLMTMMGLRDSAFWLSWGLLYAGFIFIMALFLALVIKSTQFIILSGFMVVFSLFLLYGLSLVALAFLM
SILVKKSFLTGLVVFLLTVFWGCLGFTSLYRHLPASLEWILSLLSPFAFMLGMAQLVHLDYDLNSNAFPHPSDGSNLIVA
>gi|109117480|ref|XP_001082492.1| PREDICTED: similar to ATP-binding cassette, sub-family A member 8 isoform 2 [Macaca mulatta]
MRKREISVCQQTWALLCKNFLKKWRMKRESLMEWLNSFLLLLCLYIYPHSHQVNDFSSLLTTDLGRVDTFNESRFSVAYT
PVTNTTQQIMNKVASAPFLAGKEVLGLPDEESIKEFTANYPEEIVRVIFTNTYSYQLKFLLGHEMPAKKEHKDHTAHCYE
TNEDVYCEVSVFWKEGFVALQAAINAAIIEITTNHSVMEELMSVTGKNMKMHSFIGQSGVITDLYLFSCIISFSPFIYYA
SVNVTRERKRMKGLMTMMGLRDSAFWLSWGLLYAGFIFIMALFLALVIKSTLFIILSGFMVVFSLFLLYGLSLIALAFLM
SILVKKSFLTGLVVFLLTVFWGSLGFTALYRYLPASLEWILSLLSPFAFMLGMAQLLHLDYDLNSNAFPHPLDGSNIIVA
TNFMLAFDTCLYLALAIYFEKILPNEYGHRRSPLFFLKSSFWSQTQKADHVALEDEMDADPSSHDSFEPVPPEFHGKEAI
RIRNVTKEYKGKPDKIEALKDLVFDIYEGQITAILGHSGAGKSTLLNILSGLSTPTKGSVTIYNNKLSEVADLENLSKLT

continue


Thanks if u understood and reply soon.....
............