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.......... 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....... while taking second file to search for in the first file 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 vishal