SB Molecular weight - mendessoares/BuddySuite GitHub Wiki

--molecular_weight, -mw

Description

Calculates the molecular weight, in daltons, of all protein, DNA, or RNA molecules.

Examples

Example 1

Input file: Mnemiopsis_pep.fa

>Mle-Panxα12 cDNA - ML25997a.
MVIDILSGFKGITPFKGITLDDGWDQINRSFMFVLCVLMGTVVTVRQYAGGIISCDGFTK
YSGSFSEDYCWTQGLYTIKEAYDLLTMNVPYPGVIPEDMPTCIERELINGGRVSCPDPET
VKPPTRVYHLWYQWVPFYFWLAAAAFFFPYLIYKHFGVGDLKPLIQMLHNPIVDEGDQNC
MAEKASMWLFYKLNVFMNENTIFAILTEKHRLFFIVMLVKVLYLIISILALYLTDEMFHI
GSFVSYGSEWATSLPEGDNETTLVKDKLFPKMVACEIKRWGPTGLEEEQGMCVLAPNVIN
QYLFLILWFAIIFCIACNCLSVLFALTKLVFVLGSYKRLLASAFLKDELHYKHMFFNIGT
SGRVLLQIVATNVSPRVFESIMANLATKLIAERLKGNGKGSV*
>Mle-Panxα9 cDNA - ML47742a.
MLDILSKFKGVTPFKGITIDDGWDQLNRSFMFVLLVVMGTTVTVRQYTGSVISCDGFKKF
GSTFAEDYCWTQGLYTVLEGYDQPSQNIPYPGLLPDEAPPCTPVRLKDGTRLKCPDPDQL
LSPTRISHLWYQWVPFYFWLAAAAFFMPYLLYKNFGMGDIKPLVRLLHNPVESDQELKKM
TDKAATWLFYKFDLYMSEQSLLASLTRKHGLGLSMVFVKILYAAVSFGCFLLTAEMFSIG
DFKTYGSEWIKKLKLEDNLATEEKDKLFPKMVACEVKRWGASGIEEEQGMCVLAPNVINQ
YLFLILWFCLVFVMFCNIVSIFASLIKLLFTYGSYRRLLSTAFLRDDSAIKHMYFNVGSS
GRLILHVLANNTAPRVFEDILLTLAPKLIQRKLRGNGKAL*
>Mle-Panxα10B cDNA - ML32831a-2.
MRLSEKSTSHDCKACITRSHNEDCARRWGITIDDGWDQLNRSFMFGLLVVMGTTVTVRQY
TGSVISCDGFKKFGSTFAEDYCWTQGQYTVLEGYDQPNQNIPCPVPRPPSRRGSTLNTMS
QTQGFLHNPVESDQELKKMTDKAATWLFYKFDLYMSEQSLLASLTNKHGLGLSVVFVKIL
YAAVSFGCFLLTADMFSIGDFKTYGSEWINKLKLEDNLATEEKDKLFPKMVACEVKRWGA
SGIEEEQGMCVLAPNVINQYLFLILWFCLVFVMFCNIVSIFASLIKLLFTYGSYRRLLST
AFLRDDSAIKHMYFNVGSSGRLILHVLANNTAPRVFEDILLTLAPKLIQRKLRAKDYD*

Usage

$: sb Mnemiopsis_pep.fa -mw

Output

ID			   Protein
Mle-Panxα12	45692.99
Mle-Panxα9		45619.81
Mle-Panxα10B	40727.33

Example 2

Input file: Mnemiopsis_cds.phy

 3 1952
Mle-Panxα9   ---------atgttagacatactttcaaagtttaaaggagttactcctt---ttaaaggtataacgatagatgacgggtgggatcaactcaatcggagttttatgtt-----------cgtcctgctcgttgtcatgggaacgactgtcactgtccggcaatacaccggcagtgt---catcagttgtgacggctt---------caaaaagtttggatccacttttgcggaggattactgttggacccagggactgtacacagttttagaaggatatgaccaacccagccaaaatatcccttacccaggcctccttccagacg-----aggcaccaccctgt---------acaccagtcagactcaaggacggtacgaggttaaagtgcccagaccctgatcagttgttgtcaccgacgcggatatcccacctatggtaccagtgggtccctttttacttctggttggcggctgctgccttcttcatgccctaccttctgtacaagaattttggcatgggagatatcaagcctctcgtgagattactacacaatccagtagaatcagaccaggagttaaagaagatgacagacaaggctgcaacatggctgttctacaagtttgacctgtacatgagcgaacagtcgctcctagcaagtctc---------------accagaaaacac------------ggtcttggtctatccatggtctttgtaaagatcctatacgccgcagtgtcgttcgggtgtttcctcctgaccgctgagatgttctcaattggagattttaaaacctatgg------atcagaatggatcaagaagttaaagttggaagataatctagctacggaggaaa--------aggataaactttttcctaagatggtggcatgtgaagtgaaacgctggggtgcatcaggtattgaggaggaacaagggatgtgtgtcctggcccccaacgtaatcaaccaatacctcttccttattctctggttctgtctggtattcgtgatgttctgcaacattgtctccatattcgcctccctcatcaagctcctcttcacctacggctcctaccgccgcctcctttccaccgccttcctgagggacgactccgccatcaaacaca---------tgtacttcaacgtggggtcgtcagggagattgatattgcacgtgctggcgaacaacaccgccccgcgcgtcttcgaggacatcctgct-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gaccctggcccccaagctgatccaacgg-------------------------------------aaactcagaggtaacggaaaagc-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tttgtag-----
Mle-Panxα7A  atg---ggggtggaaattctgtttcccataatcaacagagccaccgctccgatcaagtctgttaacatcgacgatttgagtagtcagctcaaccgaacttttatgtt-----------ttacttatcgctgactttcgccatcactatcaccatcaggcagcagctaggcggagcgtacattgcttgtgacggattctccagagacgaggaatatgaac---ggtttgcagaggagtggtgctggagtagtggaatctacactatcaaggaggcttatgagatgagcaacagagtcagcccttatccgggaataatcccagaaa-----atctaccagcctgt---------atagagatggagctgatatctgggggcagagtagagtgtcctgaagagaaagacgtcaagcctttcaccaggatataccaatcttggtacccatttgtgatgttttactattggctgactgctttgatgtttttcttgccgtaccagctttacaaggtctttggttttgaagacgtcaaagcggttgtagctatgttgcagaacccggtagaggatggctttgagaagaaggagctgataaaaaggggttcagtgtggctgtatcttaaatctacaatgaccctttccaacccttcagtttactcgagcttc---------------atcgtgaaacac------------agcctagctttctacgctcttactgtcaaggttatgtatttggggaacacacttcttatgtactggctgactcacaaaatgttcaagtttggatcgtttgcggagtacgg------tcttctctgggacacaa-----------gaaacccacttaacaacgtccagagccttgttcaagagaaattgttcccaaaagttgcagcgtgcgaagtaaagcgctttggtgcatcgggacttgaggaggaccaaggtatgtgcatgctggctctaaacgtccttaaccagtacctcttcttaatcttctggttctgtctccttttcgtgacaatagtcaacaccatatccctcctcctcaccctccttaacatcatctctccttgctttatgctccaacagtttctcctggcctcctctcttgataggagtccagctgtcggtgtcatatccaagctgtatcttgactgtggttcctcgctaaggttcatcatgactatatttgcttggaatgtagacccaaaattgtttggggagattttagtacagctcaactctctccttgccaaggatgaatcgcccagggctgaagtgctgaagcggcgttcaaaaaaagtgaaagttccaagtccaagaaagcctaaactcttatttcatgaagaaattaagaaaaagttaataaagaggactgaacgaaaagatgataacctaaccaatttcacgaatatgtcgaaaattagcaagaagtttgaaggcctcaaaaaaagaaatctccttcagacgaaaagcatcattaatgtaagcgttcctaagaaaatgagcgagttagaagtagaagaagatttcattcttactcctactgaagaaagtggtatccaaaacaaccctgacaccaagtatgctcaagaggatgtactggactcagagtacgtagtggtggaacaatcagtcccagaaacaatgacagagcaggaatcagtggaggaatcagtcccagagataagtaaagctgagcaagaaggcgggagctcagatcacatcgatgttgaggagaccccgccagcatcagatgttgatcgcgaagtcaactctccgattgttcagcacgaatatcaggttcagatcgacttggtttccgacgatggaagcgcccatcgtttatcgtcagatgaagctctttttccgctgcggatccctattgtgaaattgaatggcgatgttctgtcattaagatccgagagtttgcagtaa--
Mle-Panxα1   atgtactggatatttgagatttgtcaagagataaagcgagctcaatcct---gccgaaagttcgcgatagacggaccattcgactggacgaaccggattatcatgccaacactcatggtaatctgctgctttctccaaaccttcaccttcatgttcggcagca--------------acatcagctgtatcggctt---------cgagaagttggaaaggaactttgtggaggagtactgctggacccagggtatctatacaagcaaggctgcgtataacatgcc---attacatactccctacccggggattgccccctgtgtgcccgagtatgatcccgtgactcagaagtattggttaccctgtggggtggaggaagaagacaaggct-----------------------------------tatcatttgtggtatcagtgggttccgttttactttctcgctgtggccgtgggttattatttgccatttcttatcttgaagggttcaaagctgcatcaggtgaagccgctgattacgtatttgatgaaccagaggaacctggagactgatcctaaccatttggtaggaaagctatcgcattgg------------------------atcttcagacagcttgtttattcaaggtttgcggccacctctacaatcagaatgtactggcacgactgggggcttgtcctccttgtttgctctgtaaagatcctctaccttaccgtctctcttatccacctctttgccactgccaagatgttccacatcggcaactggtttacgtacgggatcatgttcgcgcggcgcagca-----------acagtcacactacccacg------------ttaaggatgtgttcttcccgaagatggtggcctgtaagatcgagacatggagtttcacagggaagaatcatcttcacgggatgtgtgttttagctctgaacgtgatgaaccaatatttgtttttgatcgtgtggtacgtcaacgtaatcatcatcttcctcaacagtatcagctgtatttacactatagtcaagttttgtagccctaacatcgttcaccaccggatagtcaactcctcctccttagacgaccaccatgactttacccgga---------tgtttggttatgtgggaccttccggacggataatcctggctaaaatgtcggaacata------------tgccggggtacatgctgaaac------------------------------------------------------------------------------------------------------------------aagtagccaagaaggtgacagagaagatagatatagagaatgaaaa--------------------------------------------------------------------------------------------------------------------------gaatagagggag-----------------------------------------agccccgactattaagtttaccaaggtt----------------------aacggtca-------gccctcagagctggccagacagc--------------------ctctcatgca-----------------------------cctgaacgctctgatgttagggatggttcctcagaatctacca-----------------------------------gaacctaaaattcaga--------atatccaacggtcgcag---------------------------------------------------------------------------------aaaaaagtacggtttctggtttaa

Usage

`$: sb Mnemiopsis_cds.phy -mw`

Output

ID			   ssDNA	   dsDNA
Mle-Panxα9		371242.6	743477.1
Mle-Panxα7A	579960.0	1158618.9
Mle-Panxα1		414459.2	828720.3