Hello Biostars, I have an assembled transcriptome that I want to align it against some conserved domains existing on NCBI. For example I want to blast my transcripts with pfam03936. Do you know how can I do that? I downloaded pfam03936 in mFasta format but could not make data base by regular command in Blast+ and Hmmer. mFasta format of pfam03936:
**>gi|301015975|pdb|3N0F|A
--------------------------------------------------------------------------------
----------------------------------------------------------------------------mrgs hhhhhhgsearrsadyepnswdydfllssdtdesievykdkakkleaevrreinnekaefltllelidnvqrlglgyrfe sdirraldrfvssggfdgvtktslhatalsfrllrqhgfevsqeafsgfkdqngnflenlkedtkailslyeasflaleg enildearvfaishlkelseekigkelaeqvnhalelplhrrtqrleavwsieayrkkedanqvLLELA---ILD----Y NMIQSVYQRDLRETSRWWRRVGLATKLHF-ARDRLIESFYWAVGVAFEPQ--YSDCRNSVAKMFSFVTIIDD-----IYD --VYGTLDE---LE----LFTDAVERW--------DV--NAIN-DLPDYMKLCFLALYNTINEIAYDNLKDkGEN----- -ILPYLTKAWADLCnafLQEAKWL------YNK-STPT-FDDYFGNAWKSSSGPLQLIFAYFAV---VQNIK-KEEIENL QKYHD---IISRPSHIFRLC----NDLASA--------------------------SAEIARGETANSVSCYMRTK-GIS
EELATESVMNLIDETW--KKMNkeklggslfakpfvetainlarqshctyhngdahtspdeltrkrvlsvitepilpfer
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
>gi|75263231|sp|Q9FYU6|Q9FYU6_9ROSI
--------------------------------------------------------------------------------
------------------------------------------------------------------------msaqvlat vssstektvrpiagfhpnlwgdyfltlasdcktddtthqeeyealkqevrsmitatadtpaqklqlvdavqrlgvayhfe qeiedamekiyhddfdnnddvdlytvslrfrllrqqgfkvpcdvfakfkddegkfkaslvrdvhgilslyeaghlairge gildeaiaftrthlqsmvsqdvcpnnlaeqinhtldcplrralprvetrfflsvyprddkhdktLLKFS---KLD----F NLVQRIHQKELSAITRWWKDLDFTTKLPY-ARDRIVELYFWIVGTYFEPK--YTLARKIMTKTIYTASIIDD-----TFD --AYGFFEE---LK----LFAEAVQRW--------DI--GAMD-ILPEYMKVLYKALLDTFNEIEQDLAKE-GRSs---- -CLPYGKEKMQELVqmyFVQAKWF------SEG-YVPT-WDEYYPVGLVSCGYFMLATNSFLGM---CDVAN-KESFEWI SRTLR---FQQRHQFICRLR----NDIVSH--------------------------QFEQKRGHIASGVECYIKQY-GVS
AEEVVTVFTEEVENAW--KDMNeeflkptafpvalierpfniarvieflnkkgdwythshaikdqiaavlrdpvti----
--------------------------------------------------------------------------------
Thank you
